I used the “Transformation” panel to slant a component, saved the glyphs file and closed it. When opening the file again the slant is gone.
There seems to be an issue when saving the file in Glyphs 2 format. Please set it to Glyph 3 format in Font Info > Other > File format version. I’ll have a look why it is not read correctly from a Glyphs 2 file.
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Changing the file format to Glyphs 3 worked. Thanks Georg!