It's not necessarily an unknown format, it's just one that your client doesn't support. This can happen when you have multiple clients using the same file system.
You could just delete the working copy you have and check out a fresh one, or you could update your Subversion to the most recent version, which is probably best.
If you want to use the script, I think it would be something like
C:> change-svn-wc-format.py D:\my_repos 1.5
where you can use 1.4, 1.5, or 1.6 as the repository version you want to use.
--skip-unknown-format means that if the script finds a version it doesn't understand in some directory, it skips that directory and continues with the upgrade.
What you should try to resolve after fixing this is how different Subversion clients are using the same working copy.