The OP is attempting to obtain competency by coming here and seeking a better way to handle it. USPAP is explicit in that one can obtain competency thru learning or getting assistance. Only Fannie requires pre-assignment knowledge. The OP, as a trainee obviously (should) have a mentor and is exploring additional thought on dealing with an unanticipated complexity. How else does someone learn?
As a follow-up, an appraiser ought to know if they are competent or not prior to accepting an assignment. However, they may discover along the way they are not. In that case, they have an obligation to disclose this to the client and detail the steps they are going to take to gain competency. The client then has the option to fire them, or proceed. An appraisers peers are persons with the appropriate credentials AND experience with both the property and assignment type. Not only am I a peer in this case, I am also a potential user type, because I too rehab properties and could be in the same situation as the OP's client is. The OP's client does not need to know what the property is worth so they can make an offer. They have already made an offer, and now the bank (seller) is saying, well gee, I don't know about that offer because we have an appraisal that says its worth more. So, the OP's client goes out to find a competent, third part opinion that they can present to the bank to show them that the property is in fact not worth as much as the bank/bank appraiser thinks, and that the offer they have made is appropriate. In this case, if the client shows the bank a junk appraisal, that doesn't beat the quality of the appraisal procured from the bank, the bank is likely not going to accept the offer made by the OPs client - hence, they have wasted their money on a junk appraisal (if the appraisal turns out to be junk).
My opinion was that the OP ought to withdraw. However, if they don't want to do that, then I went ahead and gave a detailed explanation of how they should proceed. I am a peer and also a similar user/client type in this case, so I am an appropriate and relevant resource in this case. I take it personally for many reasons, both as an appraiser and as a potential user. There is a large amount of business that could be generated for appraisers in the world of REI (I have been trying), however when appraisers accept assignments and don't understand how investors operate or what they need, it hurts our profession. And for the record, and also stated in the original post, (probably) all of us have made the same mistake. It sucks. Take your licks and move on.
If any of you want to scold me for all of that you go right ahead and my response is you can go jump in a lake.