I have been experiencing the same problem described here, IntelliJ is unable to link source files to class files when the source files are clearly there. Some classes seem to have source files, and others do not, something that seems to be determined by some hashing algorithm. Has a fix for this problem been found?
EDIT: After using a slightly different search term I think I found a solution to my problem. Apparently refreshing IntelliJ's caches fixes it, at least temporarily? However unexpected this fix is, it seems to work. I would have guessed the things I tried would have invalidated IntelliJ's caches, but I guess not.