It seems like this game is having the issue that CB20 had with coaches being removed/added messing up the file upload. The .pbb file is getting updated on the FTP site but the coach files are not and the new ones are not getting added and deleted coaches aren't getting removed.. I know its failing (partially) because I get an error despite also receiving a file upload successful notice.

I found a solution and maybe you can use this to help you write in a fix... your coa sqlite files are not getting closed out. The shm and wal files still exist even after saving the game. If you close the game out, the shm and wal files disappear and then you can re-open the league and publish the files. Coach files get published correctly as well.

UPDATE: it also closes the coach database files when exiting to the main menu.. so they're not getting closed somewhere in the code.