Red Flag after font import

I’m working on a font family that does not need compatibility and I turned compatibility check off. All was good. Then I imported a variation of the font I had worked on earlier to create a new master that was a little more freeform. It made red flags show up on a bunch of characters in all the masters. So I decided to delete the new masters I added and not use that option. Once i deleted the new masters, more red flags appeared. I decided to updated metrics, info, and features. Glyphs crashed. Now there are red flags on every character in every master even with compatibility off. But it still works and exports fine. What could the red flags be?

Can you send me the file?

I will send the broken one. But after working with it about an hour more, then clearing out exports and re-adding the exports it is now working. I’m not sure what “broke” it or exactly what fixed it.