Hi Gaule,
I believe, your father's visitor visa must have expired by now if it was stamped on Feb of 2019. I do not know if that is acting against the adjustment of status that you did not take action early on to extend the visitor visa while he was here. To my experience each of the USCIS counselor is different, some may overlook the expiration date and process the adjustment since you are a US citizen, and some may just act according to what is black and what is white in paper. The birth certificate was missing and then like Ark said, the RFE thing is dumped so they rejected. I can not say for sure if the expired visitor visa (?) was a deal breaker here completely.
I would recommend you to call USCIS people if possible. Remember they are very wooden people to talk to with no emotions at all, most probably because they handle 1000s of cases like yours in a day and different. See if you can explain your case and if they can suggest you any way out. Since you said you filed appeal already so that might work without your father having to leave the country, maybe.
If you can check out this laywer's column from New York, he is quite insightful and helpful with his answers, back then I used to follow his column in New York Daily Post. You can even email him, he may or may not personally email you back, but I used to see Nepalese people students asking him a lot of immigration related stuffs. His twitter handle:
https://twitter.com/awernick?ref_src=twsrc%5Egoogle%7Ctwcamp%5Eserp%7Ctwgr%5Eauthor

His Column in the paper:
https://www.nydailynews.com/allan-wernick-staff.html