rmdir dir gives error 'Not a directory'

It's impossible to know what happened given that the evidence is now deleted. Your descriptions of the symptoms is consistent with dir2 being a symbolic link to a directory. A symbolic link is a sort of special file that says “the real file is actually over there”. The symbolic link itself isn't a directory, so rmdir can't do anything with it. But accesses to the content of the symbolic link (files in the directory for a symbolic link pointing to a directory, file contents for a symbolic link pointing to a regular file) go to the target of the link transparently, so you wouldn't have noticed anything when using cd dir2 or when editing files in the directory.

If this is the case (which is plausible, but not at all certain!), then the command rm -r -f dir2 only deleted the symbolic link, and the directory containing your changes still exists… somewhere. Since you've deleted the link, it might be difficult to find where, but you can try looking for the file names that you know were in that directory with the locate command or with an equivalent GUI (Spotlight?).

In the future, run

ls -ld dir2

That would tell you what kind of file dir2 is. If the line begins with d, it's a directory. If the line begins with l, it's a symbolic link, and the output indicates where it points to (the part after ->).