I noticed after upgrading to Krita 4 that the hidden layers inside a group are not effected when transforming the group, I don't know if this was the case in Krita 3 but I can't remember it being a problem. the work around is just to show all the layers / groups, but It's really annoying as my workflow makes heavy use of grouping, layer / group visibility and the transform tool.

That definitely is a regression. Please do make a bug on bugs.kde.org about it. I've checked the code and the warning about invisible layers also getting transformed is still there, but they aren't transformed.

Thanks for the quick reply. I'll see if I can figure out how to make the bug report.