Well if you had to re-register, something was majorly wrong since accounts are in dbo... Though if you don't really have a problem with it as of now, there's no point in talking about it.
You also actually do NOT have to 'copy/backup/transfer' (whatever you wanna call it) uniquenamed, the ONLY one that is REQUIRED (to save characters) is DBDATA/GAMEDBD... Some people can disagree with me all they want, but uniquenamed will re-populate itself automatically once you run your restored game DB... This has never caused issues in the probably THOUSANDS (1,000's) of times I have done it this way (NOT copying or 'backing up' uniquenamed')...
Now, with that out of the way, make or take your backup of the game DB data and delete clsconfig from the 'backup'. You will want to go from an 'empty' server installation (with no DB files at all) and start the daemons so that it creates all of the game DB files as it automatically does. Next step STOP all daemons. Following step, COPY your backup (WITH NO CLSCONFIG) to your 'running' DB directory (over-writing) the empty ones that running the daemon created... Presto your problem will be solved
