How to fix the bags without starting from scratch after GU45

[gm9]

If all your toons use the same layout just delete all their uisettings.ini files (except the one you fixed of course) and select the fixed one when you log in.

Otherwise you will have to do them all manually. However, if removing all bag entries helps, just compare the fixed file with the previous ones and see which entry was the culprit. That way you only need to remove that one for your other toons.