According to this post:
The "not a valid repository" error only arises
when Fossil tries to measure the size of the repository file and sees that
either the file does not exist or else that the size of the file is less
than 1024 bytes. It does this by calling stat() on the file and looking at
the stat.st_size field.
it seems likely that you have a missing or truncated Fossil file. Make sure you've actually deleted the repository file, and that your filesystem has actually released the file handles. Fossil stores some respository information in ~/.fossil, so you may need to remove that too.
rm ~/.fossil
In egregious cases, you may want reboot after deleting this file, just to be sure you're working with a clean slate.
If you're still having problems, try creating a new repository file in a different directory. For example:
cd /tmp
fossil init foo.fsl
fossil open foo.fsl
fossil close
If all that goes smoothly, you'll have to hunt down whatever remnants of the repository are lurking. As long as the file handles are closed, there's no reason you shouldn't be able to delete foo.fsl (or whatever) and call it good.