I am inclined to agree with DANRVAN about the value of real estate versus depreciable equipment. Under theory, the equipment is worth less as time goes by, whereas real estate increases.
What I ended up doing: Allocate the original value spent on the s. 1245 when new, subtract this from the total sale, and the remaining price is thus allocable to the s. 1250 assets. The result: s.1245 gains were depreciation recapture and ordinary income, and there was significant capital gains on the real estate as well as s. 1250 recapture capped at 25%.
Something else to think about, and it's not very professional. I often wonder what an auditor would do and whether he/she would go to a lot of trouble creating an adjustment. In this case, the lack of an appraisal might cause heartburn with the auditor, but then he/she would have to write up an adjustment. In other words, in order to do his/her job, the auditor would have to use appraisal techniques and suffer from the same lack of appraisal as the preparer. My experience is if an auditor is confronted with a difficult and time-consuming detail with questionable results, they are inclined to back away.