There is probably no need to include Form 1040-X with the filing of the 2020 and 2021 Forms 5329. There are no other changes to your filed tax returns for those years, so Forms 1040-X would serve only to show that there were no other changes. However, because the code PJ 2022 Form 1099-R would normally be reported on your 2021 tax return, it might not hurt to include Form 1040-X with your 2021 Form 5329 just so that you can to explain that the $647 is not taxable on your 2021 tax return due to you treating the code-PJ reporting as erroneous.
Of course you could try to get Schwab to correct the code PJ Form 1099-R to show $0 returned and issue a new code-J Form 1099-R for the gross amount distributed, but given that they goofed this up to begin with by not rejecting your request (or instead treating it as a request for a regular distribution in the first place), I probably would not expect them to be competent enough to do that properly.
