So I have tried the solutions given, but there just is no fix for this issue.

Yes it only happens with FF14, and all characters, and the controllers are 1st party.

The problem lies with how controllers are coded with FF14 on pc, and unfortunately the only realistic option imo is for them to change how devices are discovered on pc. Just code it the same way that it's coded for every other game available, where it doesn't disconnect your controller when your pc attempts to refresh because it thinks a new device has connected. I don't understand why this is an issue that has been in the game for so many years.