So, here is fixed version, now topmost clipped layers in group and project should not break projection rebuild. Please let me know does this fix help?
Linux appimage:
https://github.com/uvhat/krita_clipping_layers/releases/download/krita_clipping_layers_5_3_2_1_c15/krita-5.3.2.1-97e88e6e23-x86_64_c15.AppImage
If you will find any bug related to clipping or other mods please let me know!
Description and diffs: