Remove overlap command removes straight segments with handles. GSLayer.l.removeOverlapCheckSelection_keepOpenPaths_gridSize_error_() reduces cases in diagonal segments, but not the completely horizontal or vertical ones.
Is there a way to prevent it?
You mean it removes the handles from the straight segments?
Keeping those handles should be even the default IMO. Especially with potential variable font setups in mind.
Yes, Glyphs removes handles from the straight segments with handles; it feels like it’s applying Tidy Up Paths as part of the function.