Hi @Nate Shields,
I think most here are misunderstanding your question.
Your issue is that your property is not grandfathered in it's zoning status. That is generally fine, although a bit of a risk when purchasing a property with the incorrect zoning (for MF at least).
-First, I would use this to negotiate a much lower price on the property
-Second, check and make sure that the current owner did not try to have the property rezoned and fail. If they failed previously then it is a much larger risk.
-Third, Before rezoning the property, see if there are under-utilized areas you want to use to make it let's say 23 units instead of 20. Or even check if you want to merge some units. Hard to discuss without seeing plans.
Finally to answer your question, yes this will be an issue if you go to sell it down the road especially if you or someone else has failed trying to rezone the property. Typically with MF there will be no other uses for the building other than tearing it down so it shouldn't be too difficult to re-zone depending on your locality.
If you have more questions you may PM me as well.