I have tried tinkering with the mess that I have to no avail. I have discovered one big mistake that I have made. I made a backup copy of all of the links sql on a cd. But I did not run an import/export backup of the defs.

Result being that now my categories are missing on the original version. Not sure yet what else might be missing.

So for all other rookies out there be sure to run a import/export backup.