I dont know why, the uppercases appear to have 2 unicodes, one is the actual uppercase glyph and the other is for the lowercase (see screen) and when try to edit the lowercases, it opens the uppercase. Is there any way to fix this without deleting them by hand?
I still do not understand what the problem is. Select all and update glyph info as described, and the uppercase will get uppercase codepoints, and the lowercase will receive lowercase codepoints.