In the Responsa below Rabbi Fienstien explains that food does not necessarily become non-Kosher if cooked in non-Kosher utensils - that is utensils used previously to cook non-K food. Notwithstanding, we are not permitted to cook with such utensils nor may we commission a non-Yid to manufacture Kosher foods in such utensils.
Foods prepared in defiance of this ban are prohibited by way of penalty, but only to those who defied and those for whom the ban was defied.
This means that potato crisps for example, that are made with Kosher ingredients can be Kosher despite being cooked in non-Kosher utensils. However, these same identical crisps, manufactured for a Kosher label or brand, would not be Kosher.
Rabbi Moshe Fienstien, Igros Moshe Y"D 2:41 There are factories producing non-Kosher margarine that comply with strict cleaning regimens in order to retain the quality of their production and thus their successful business reputation. Furthermore, they are strictly monitored and enforced to abide health regulations that bear significant penalties if breached. The query is: does such cleaning permit producing Kosher margarine upon the cleaned machinery?
In my humble opinion, if the cleaning regimen employed to satisfy their own quality standards and the standards set by the health regulators, meets the Halachic temperature requirements, it may be relied upon to thereafter manufacture Kosher margarine. Proof for this can be derived from the Gemara A"Z 30 where regarding what is considered a health risk, which the Halacha treats with greater caution than matters of Kashrus, Halacha does not require supervision [but relies on the safeguards taken by the non-Ys to maintain hygiene]. This guideline is well accepted amongst the Poskim who use this Gemara as a source even for cases of potential Torah prohibitions.
Now in our case we may certainly rely upon their procedures to deem the machinery “Koshered”, since the owners are motivated for their own benefit and will without doubt ensure that the cleaning regimen is closely adhered to. Additionally, our concerns are only of Rabbinic nature since any flavour absorbed within the machinery is "Eino Ben YoMo - more than one day old" and therefore tainted [and unable to contaminate and disqualify the Kosher production].
[Non-Kosher flavour that is absorbed in a vessel can be either fresh or stale. If it is fresh i.e. Ben YoMo – of that day, it can render other foods that it contaminates, non-Kosher. If it is stale i.e. Eino Ben YoMo, it can not. A stale taste does not qualify as non-Kosher. Nevertheless, our Sages OBM prohibited cooking in vessels that are Eino Ben YoMo - old and thus tainted, not because the food will become non-Kosher but to prevent us inadvertently using such pots when the flavour is still fresh, Ben YoMo.]
I should mention that actually there is no need for "HagAlah - purging" at all. It would suffice to use clean machinery for the Kosher batch, since the absorbed flavour which is "Eino Ben YoMo” - old and thus tainted, does not render the food un-Kosher.
This is clear from the Gemara of A"Z 38 which permits us to consume oil cooked by non-Ys in their non-Kosher pots, based on the assumption that such pots are "Eino Ben YoMo - old and thus tainted". This clearly illustrates that foods cooked in non-Kosher vessels can be Kosher.
[It should also be noted that although detergents and degreasers were not available in those days, we assume that their pots are clean or clean enough to not contaminate the foods cooked in them.]
Although our Sages enacted a decree prohibiting "Eino Ben YoMo", the prohibition bans USING the vessels. It does not, as we just explained, prohibit the foods cooked in them. Our Sages did impose a penalty banning the consumption of the food but only by those who deliberately violated the rule, those who deliberately cooked in such a vessel. The penalty also applies to those for whom the food was cooked. Thus, any Jew, other than those who cooked it and those for whom it was cooked may eat food that was knowingly cooked in a non-Kosher Eino Ben YoMo pot.
[So to put some flesh on the formula of this Law: if our non-Jewish neighbour offers us some fruit cooked in her non-Kosher kitchen, it is Kosher. However, we may not request that she make some for our son’s Bar-Mitzvah party. If we did and she did, then we and the invitees to the Bar-Mitzvah party may not eat her cooked fruit. We may however, take it to Shule and offer it to the rabbi and the congregation.]
Consequently, since the factory and the margarine both belong to a non-Y, who is not restricted by the ban against using Eino Ben YoMo vessels, the margarine is Kosher [even though it is certainly made exclusively for the Kosher market]. Neither is the non-Y acting under a Jew’s instruction to manufacture the margarine and it most certainly can not be disqualified simply because a Jew supervised its production.
I have seen though, that the PisChey TeShuvah 122:5, suggests that if a non-Y of his own initiative, cooks food for a Jew in a non-Ben YoMo pot, it is nevertheless prohibited. Now I have looked carefully at the sources brought by the PisChey TeShuvah, and in my humble opinion it appears that both sources he quotes actually permit the food.
Indeed, the case he quotes from the MaHaRam of Lublin is far worse since in that case it is not an absorbed non-K flavour that may be contaminating but actual prohibited substance that is less than 1/60 which may be contaminating the Kosher food.
[That case questioned milk, collected from a herd of animals under the watchful eye of a Jew but the beasts themselves were actually assumed to be non-Kosher since they as a herd had been attacked by wolves and were accordingly all deemed to be non-Kosher, Tereifos. The milk of this non-Kosher herd, which is also not Kosher, had been combined with more than 60 times its volume of Kosher milk.]
Now the case discussed by the MaHaRam should be prohibited as per the Shulchan Aruch [YD 99:5] that forbids by Rabbinic decree, deliberately nullifying prohibited foods in 60 times their volume of Kosher. Not only is combining them prohibited but the mixture also becomes prohibited. Non-Kosher that is deliberately combined with and thereby nullified to Kosher, is banned both to those who nullified it and to those for whom it was nullified. Nevertheless, the MaHaRam permits this case since a non-Y nullified it. His reasoning is obvious; we penalise those who flagrantly violate the Sages’ decree. The food is banned in spite of its being Kosher [It is Kosher since after all, the non-Kosher component is nullified]. However, a non-Y, notwithstanding his acting for the benefit of a Jew, is not subject to these restrictions and penalties.
However, we may not instruct the non-Y to cook in his non-Ben YoMo pot, since this is tantamount to the Jew cooking it himself. As the PeRi MeGadim notes, if we instruct a non-Y baker to make a cake which includes spices that have been crushed in a non-Kosher grinder [and are therefore non-Kosher], we may not consume that cake since it is tantamount to adding the spices with our own hand. Now, if Kosher spices are also available but the baker uses the non-Kosher for his own convenience, it is certainly Kosher even though the baker is instructed by a Jew to make the cake. The Jew did not instruct that spices crushed in the non-K grinder be used.
We are only in violation of the Sages’ decree if our instructions are tantamount to directing the non-Y to use non-Kosher spices. When non-Kosher spices are the only ones he has and we direct him to make a cake, it is as good as directing him to add the non-Kosher spice, since this is the fixed recipe. However, if the baker has Kosher and non-Kosher spices then we may direct him to make the cake and we can eat it. [The same is true if he does not always add spice to the cake or perhaps even if we tell him we don’t mind if he omits the spice.]
Similarly, if we do not instruct the baker to make the cake [we purchase cakes made for the public even if the clientele is predominantly or even exclusively Jewish], the Sages decree has not been violated, no penalty applies, the cake is perfectly Kosher.
It must be noted though, that this penalty is not found in the Gemara (A"Z 75), nor in the RaMBaM (M"AsuRos 17:2) and Poskim, nor in the Shulchan Aruch (Y"D 103:5 & 122:6). The source seems to be the RaShBA, quoted by the Beis Yosef, which I found in Toras HaBayis HaAruch 4:4. However, the Beis Yosef himself does not include this in his Shulchan Aruch neither does the Ran (Chullin 7) who indeed quotes the initial words of the RaShBA but significantly omits his conclusion that the food may not be eaten. So it appears that they do not rule according to the RaShBA.
Indeed, the RaShBA's reasoning that cooking in a non Ben YoMo pot is comparable to adding negligible proportions of non-Kosher food, seems to be flawed. In the eyes of the Halacha, non-Kosher foods are only those that are discernible flavour and food enhancers. Their effect is relevant when their proportions are significant. Consequently our Sages prohibited deliberately adding even insignificant doses of such non-K foods. Furthermore, to protect this our Sages banned the food if the non-K is knowingly added. It is therefore actually Kosher but prohibited only to those who made it and for those whom it was made.
On the other hand, non-Ben YoMo flavour is not a viable flavour or food enhancer. Non-Ben YoMo flavour does no more than prohibit us from using the pot in which it is absorbed. It is identical to the prohibition of using a vessel that has not yet been immersed in the Mikvah; we may not use it but using it does not prohibit the food. The reason for this is that non-Ben YoMo flavour is in fact not at a flavour at all and even if the pot was used in defiance, the food would still be acceptable.
One may adduce proof for this from the DarChey Moshe 122:2, who explains that the assumption that a non-Y's cooking vessels are non-beney-yoman applies equally to the utensils of a Jew. Yet the Halacha differentiates between the two.
The difference is that the vessels of a Jew can be investigated and determined if in fact they are or are not beney-yoman [Sh"HaGiborim A"Z 8]. For not investigating we are penalised and must consider the pot a Ben YoMo whose absorbed flavour is still fresh [and will contaminate]. If we were to penalise one who uses a non-Y's Ben YoMo pot the DarChey Moshe could not suggest a difference between using a Jew's or a non-Y's pot.
It is however clear that the flavour of a non-Ben YoMo pot can not disqualify the food cooked within it. Such penalties are imposed only for defiance.
It thus emerges that A), the majority of rishonim and the Sh"Aruch do not agree with the Rashba. And B), even according to the Rashba, Jewish supervision will not be cause the food to be prohibited. However, if the manufacturer is contracted to make a Kosher batch, then according to the Rashba only, will the food be prohibited unless the plant is Koshered.
Although as explained, foodstuffs not expressly made for the Kosher consumer do not require Koshering of the plant, nevertheless it is shameful to offer Kosher certification without Koshering the plant. This is not a word for word translation of the The Teshuvah. I have tried to convey the tone as well as the substance and have included in  additional comments that provide helpful background information or clarify or emphasise Reb Moshe’s thoughts.