Not sure if this is in the right part of the forum, but when I try and merge an overlay layer to a normal layer then Krita just shuts off without warning and without appearing as if it has crashed. There's not even a "Program is unresponsive" message, it just blinks out and I have to reload the entire program to start working again.

Has anyone else experienced this issue? Is there something I need to do differently to be able to merge those layers?

Thanks for your time.

This is indeed a bug, there's no reason for Krita to crash.
You might want to report a bug at bugs.kde.org.