Were you deleting folders when it was happening before?
Quite probably. I move stuff around quite regularly.
Does it work when you remove them from Hazel and add them back in
I don't think so.
I had linked to a "Music" directory on an external drive but then decided to move all my music back onto the startup SSD( the mac osx "Music" directory).
I then deleted the external hard drive "Music" directory. When I opened hazel today it was the external "Music" directory that it had identifed as Missing and the groupings had gone.
I subsequently relinked the startup SSD "Music" directory but the grouping didn't return.
I have now created the other missing directory and again launch Hazel. The grouping did not return.