When I use the Fill Tool on a group layer, it turns invisible all what I've done on those layers (not the layers themselves). Undoing won't bring back what I've done, either partially or at all. It does, however, when I toggle Passtrough (on group layer) or turn off and then on one of the layers.
Thanks for your report! I am able to reproduce the issue.
When retesting this a moment ago, I found that you need at least two layers in the group for the bug to occur.
Git commit 17a60a84674e3b12e681399bd88aabaa30d2738a by Boudewijn Rempt. Committed on 30/09/2017 at 14:55. Pushed by rempt into branch 'krita/3.3'. Don't allow the fill tool to work on group layers This fixes the issue where it would be possible to apply a fill on the projection of a group layer, leading to really weird results. M +1 -1 libs/ui/tool/kis_tool_freehand.cc M +22 -20 plugins/tools/basictools/kis_tool_fill.cc https://commits.kde.org/krita/17a60a84674e3b12e681399bd88aabaa30d2738a
This was already fixed in master.