When I add unicode value (from PUA) to ligatures, the dlig feature disappears if I update the features. Adding it back doesn’t generate any letter pair replacements.
Adding unicode value to stylistic alternates and swashes works fine.
I’m using Rainer’s script to add PUA unicode values.
What do you need the PUA codes for? I recommend not to do this.
The dlig feature relies on the category/subCategory and the PUA code mess with that. Maybe manually resetting them might help.
I’ve always assigned PUA unicode to ligatures for those users that use applications without opentype support such as silhouette, cricut, canva etc. Wouldn’t do it if I didn’t receive quite a few requests of permanent basis. It worked fine in Glyphs 2.