I am not certain how bonus depreciation factors into this transaction since it is not allowed for residential rental real estate. I am also not certain why a 4797 was generated unless there are additional details you did not provide.
Frankly, you should try contacting Support, via the link below, since you appear to be struggling with getting the exchange entered properly. Support has helped other users enter exchanges in the correct manner.
https://ttlc.intuit.com/community/using-turbotax/help/what-is-the-turbotax-phone-number/00/25632
