Something’s happened with my Glyphs, with Glyphdata while I was working on a font. I didn’t touch glyphdata.xml, I’ve just opened EditGlyphData to check some names and then the anchors started to reset at strange places, like top anchor at ascender line for all glyphs. Also, .case accents stopped to work automatically on Create Composite
It might be better to make a copy of the file when working with it. Because if you change it, it will invalidate the code signing and Glyphs will stop working.
Solved it in a Zoom session. For reference, it was a custom GlyphData.xml interfering.
And it was glyph data written for Glyphs 2, which had no letter case information the way Glyphs 3 would expect it. So the top anchors defaulted to the ascenders etc.
Yeah, it was a custom GlyphData.xml for Glyphs 2 in a parent folder to my font file