I’m unable to try to reproduce the issue right now so I’ll be making quick guesses and suggestions now. Maybe it’s an issue in Windows Explorer (or more specifically in its WebDAV implementation) or maybe it’s indeed something in Cryptomator.
Check out the log file in %appdata%/Cryptomator/cryptomator.log. Are there any suspicious errors?
In any case, a quick solution could be to use Cyberduck to rename the long filename into something shorter. After that, Cryptomator should be able to populate the file list in Windows Explorer again.
Edit: Copy the WebDAV URL in Cryptomator, see Can I use alternative WebDAV clients? and then paste it in Cyberduck’s “new connection” window.