Are the cells of the baby, once it’s mixed with the virus, part of a new substance and that’s why it cannot be separated?  If so, then the fetal cells no longer exist.  
.
2 parts water mixed with 1 part hydrogen = water.  If you add another part of hydrogen, you have an entirely new substance - hydrogen peroxide.  Water no longer exists.  You can’t say, “Well, the “water DNA” still exists”. No, it’s an entirely new chemically altered thing.  
.
If the fetal cells are used/consumed in making the virus strain, then it doesn’t matter if traces of the DNA still exist because the end result is a new thing.  

1) CONTINUING sin.  As the one article cited by Sean points out, we're not talking about a remote material participation in some past sin, but an active participation in a current sin.  To the extent that remnants of the murdered child remain in the vaccine, we are actively participating in the abuse and desecration of a human body.  Let's say that the nαzιs killed some Jews and made lampshades from their skin (assume for now that this actually happened).  I didn't agree with what they did to the Jews, but I decided to acquire one of these lampshades and have one of them on my coffee table.  Whether or not I agreed with or participated in the murder itself, I am participating in an ongoing sin against the dignity of that person.  Likewise, going back to my car lot example.  I want a cheap car so I buy one off a lot where I know that all the cars are stolen.  Well, regardless of whether or not I participated in the original theft, by owning this car that I have not right to own in justice, I am continuing to actively participate in the injustice committed against the original victim.

What about this hypothetical? Mr X is a wealthy man. Mr Y kills him for a personal reason. Mr Z, Mr X’s heir, is aware of Mr Y’s plan but does nothing to stop him because he wants his inheritance. Let us further assume that Mr Z’s role is publicly known but that for the sake of this hypothetical he is not found guilty by the law nor suffers any civil penalty. He uses his ill-gotten wealth to establish a legitimate business. Thirty years later, a father of a family can only get a job at this business. Can he licitly take the job?

So of the 3 points I cited, Pax's one argument pertains to this one here, that no actual remnant of the original baby remains, that what remains is an entirely new substance.  I believe that the respect that must be shown to human remains pertains even to the purely-material remnants of the body.  If a corpse has been cremated for instance, and all that remain are ashes, certainly it no longer has the form of the human body, but is it OK then to put these in a cat's litter box to defecate on?  Recall that at the Resurrection of the Body, God does obtain the original matter that constituted the human body to re-created the risen bodies.  Also, the body itself loses its human form when a person dies, since the soul is the form and the body the matter of the human being.  So I believe and hold that even the matter of a former human body must be respected and cannot be desecrated.

Involuntary mask wearing—as when shopping—might be a distasteful concession to an authoritarian and Christophobic state, but it is a concession that neither implies nor necessitates a surrender of a high principle or a moral absolute.

Bump for Pax.