The data for toolboxes are stored in file Wcmdmap.db found in the Multi-Edit\Config folder. Perhaps you have a backup of this file you could use.
You can also view this file in Multi-Edit by going to MACRO -> RUN… or clicking on the and entering the command SWITWIN /SYSTEM=2.
The first section of this file lists all the commands that get listed when you do TOOLS -> CUSTOMIZE -> KEYS/COMMANDS. Each command is given a number. Then there are some entries for toolboxes, interspersed with entries for menus. This is the data that gets listed when you do TOOLS -> CUSTOMIZE -> MENUS, or TOOLS -> CUSTOMIZE -> TOOLBARS/BOXES.
If there’s corruption it’s in the Wcmdmap.db file. If you have an eariler copy of this file you may be able to figure out what’s wrong. Maybe you ended up with two entries for toolbars of the same name, or something like that.