After modifying some of my boxes in PKHex to have the (100% legal) Pokemon I wanted, and injecting the save back into Sword, I noticed that when I transfer a Pokemon to Pokemon Home, then boot my copy of Sword back up, that Pokemon is present in the box slot, but it's also still in Home. When I transfer a Pokemon from Home to Sword, the Pokemon is gone from Home, but isn't present in Sword either. (I haven't lost anything too valuable thankfully, but I assume the few Pokemon I did transfer are gone forever.) When I move a Pokemon from one box slot to another in Sword via Home, the changes are not saved either - the Pokemon is present in its original slot and absent from the slot I moved it to. Any idea what's going on here?
If it helps, I injected the save by ripping it with EdiZon, editing it in PKHex, restoring it with Checkpoint (I was having issues with EdiZon at that point), locating and backing up the save files with Tinfoil, mounting my Switch's sysnand, and replacing the previous save files with the new ones. It seems to have worked in that I'm not banned, but the interaction with Home has me quite worried. Seems like Home can't save changes to Sword for some reason?
Also, saving in Sword and reloading does keep the saved changes. It's only saving Sword from within Home that isn't working.