So, question, was this after you clicked "yes" to a windows prompt asking you to elevate the FFXIV launcher so it could change files/patch?

If so, that's probably why. It's similar to "run as admin" - other programs don't have the permission/authority to touch it when it's in the mode. If this is the issue, restart FFXIV and it should work again. (This can also cause issues with other overlays, like Steam, Discord, etc)