[BUG] Discarding all my changes whilst connected to a repo with various sub-module where one I don't have credentials for, clears all links to my existing sub-modules.

Exactly as the title states. I discarded my local changes to pull in the latest from my remote, an error relating to the one module I don't have credentials for popped up, and then suddenly all my sub-modules vanished and I need to add them all manually again.