FYI, for everyone else - he was able to fix it by deleting the contents of his c:\users\(username)\.TRIGGERcmdData folder. Then when he ran the TRIGGERcmd Agent, it re-prompted for a token and re-created his computer in his account.
In hind-sight he should have backed up his commands.json first (oops).
Also, the server I'm using this on hid the task bar icons, so it was a little while before I realized there was a place to right-click and pull up a GUI editor =P. The directions on your website are not incorrect.