First, how far back do the building permit records go and when was the conversion done. I say this because at least in my state, permits only go back so far and if there is the potential that the conversion pre-dates the amount of time the records are kept, there is no way for me to adequately determine whether it was permitted or not.
If it clearly is not permitted, then I would only proceed with completing the report "subject to" repair/alteration under an HC or appraise it "as-is". This nonsense of "figure out a cost to cure to convert it back to a garage" may not only be beyond the appraisers competency level, it may actually be contrary to how the market reacts to unpermitted conversions/additions. If the market considers it to have contributory value, then that is how I'm going to appraise it, with disclosure as to how the market currently reacts to unpermitted additions and/or conversions. If a typical buyer or seller would find it unreasonable to convert it back and/or remove it, why should the appraiser? If this is not appropriate per the clients guidelines, then at that point I would decline the order for no other reason that it is an unacceptable assignment condition, in my opinion.
Of course, if your market is different and the local municipality actively penalizes "illegal" additions or conversions, if homes can't be sold if they're in place and/or buyers and sellers would find it reasonable to remove/convert back to what is "legal", then I guess you could appraise it the 3/2 way, but I still would probably only appraise it "subject to" unless I was given bid(s) of what it would cost to remove/convert.