Since I wasn't expecting this to happen, I didn't take notes of the exact sequence that led to this problem but I have at least two files that are now uneditable in my project. They were both named something different but I have renamed them. I did this by closing the buffers on them, renaming them outside of SE, then going into the project properties, removing them from the files list then adding the files under their new names. Now, I can open them but if I try to do some things on them (go to references, scroll a ways down), the buffer is replaced by one from a different open file. If no other files are open, the buffer is for .command.
I haven't tried anything to make the problem go away, such as removing them from the project and re-adding them or recreating the project, although I have restarted SE a few times since it started. It does seem to be persistent.