Hi yes, so wow it's been a while, but yes my wife did eventually get her AP after about 11 months, I mailed her the AP and she used it to come back, there were no issues and no questions at the port of entry (SFO).
So afterwards, we double checked with our lawyer, and her recommendation was that we re-file our AOS, because technically, the original AOS is considered abandoned. On the safe side, we filed a new AOS so we had 2 AOS applications active at the same time.
When the time came for the interview (this was about 4 months ago), our lawyer recommended to be completely truthful and tell them exactly what happened. So we told them about her leaving the country without the AP, and explained why we had 2 active applications, etc.
So the interviewer agreed that the original AOS should be considered abandoned, but he said he can still do the interview for us (so the interview would actually apply to the 2nd AOS, even though that one is still going through the process). He said once the 2nd AOS reaches the local USCIS office, hopefully he can just apply the interview to that one, and not have to do a 2nd interview.
So that's where we are now, just waiting for the results of the interview. Bottom line is it became quite messy, but I think in the end we did the right thing and tried to be honest and transparent to USCIS throughout the whole process.