I assume that upon resetting the H9 I should go to "restore purchases" to get it to return to an H9 Max, or has it already been branded that way since originally updated
Resetting your system settings won't affect your algorithms. That should still all be there after a system reset (or a factory reset), but if you ever did have any problem like this, the restore purchases function would sort this out.
By the way the Boss FS-5U has a polarity switch. You didn't change the position of this switch did you? If I were you, I might try setting the H9 to expect just an aux switch and then connect the FS-5U directly to the H9 to see if it was working correctly. But I'd also reset the system settings as Nick suggested above.