I haven't reported the missing messages thing anywhere as I assumed that was just expected (IIRC (and this is a big IIRC) it was mentioned a long time ago (i.e. entirely unrelated to this) by TravisR on Discord bridge problems as a possible cause for missing messages).
Here is one event in an affected room, made by a t2bot.io account on July 6, to which t2bot.io accounts can reply to, but which gets an "Event not found." error when requested by me, @dzaima:matrix.org: (and for reference t2bot.io functioned properly on other rooms during that time, so overall t2bot.io↔matrix.org federation should've been fine; and for reference there's a third homeserver that federated with t2bot.io fine in that room just fine too; and to be clear the room works fine now)
https://matrix.org/_matrix/client/v3/rooms/!WpdazzauuDxyGNAiCr:matrix.org/context/$BM9s8e3vUhk_iHfdg7D_s7CsQ5COFSPdlJdygz7TKvU