Obviously, you know your own code better than I do, but just in case it might save you some time digging, I believe the issue is in line 694 of fuzzy_file_nav.py. Togging with super+h toggles ignore_excludes, but it does not impact show_hidden. There seems to be some unintended overlap between the meaning of “excluded” files (by regexp) and “hidden” files.
I’m not sure what the right resolution is. I want to be able to change showing and hiding all files, hidden and excluded, through toggle, but there doesn’t seem to be a clean way of doing it with just one toggle. Maybe keep super+h for toggling hide files and have another command to toggle excluded files? Or if it is easier, just change super+h to toggle show_hidden instead of ignore_excludes, since it is probably much rarer to want to load an excluded file than a hidden one.