I don't really understand this behavior:

When I change a a default brush to my liking, then click "overwrite brush" in the "edit brush settings" window, the brush will complete vanish from "My Favorites" and all other brush preset groups. When I change the preset to "All" I can scroll down and find the brush. But when I right-click on it and hover over "remove from tag", "My Favorites" and others are listed as it's tags. I tried switching one of it's other preset groups and the brush is nowhere to be found. The only way I can find it again is by going to "All"

I thought that "overwrite brush" was just for saving the changes you made to that brush as a new default. It does that, but the behavior of it disappearing all of it's preset groups really seems like a bug. Was unsure if this should be posted here or in the development section.

There are two bug reports on this, the original is here: https://bugs.kde.org/show_bug.cgi?id=401634

It doesn't happen for everyone and it's intended that it will be dealt with by the upcoming reworking of the resources management facilities.

Thanks, good to know that it's being worked on. I hope they come up with a good solution. Are they accepting suggestions currently?

I don't know but you could present any ideas you have in the Krita Development forum.