I posted this elsewhere since it is been a problem since Lion. There is a script that is supposed to update the list when you delete them, but it still hasn't been fixed even in 3.1.1. I reported it months ago by esclating up to Apple's enterprise service desk. I suggest you all do the same as we should have to do this outside the GUI. Here's a modified version of what I posted in the old Lion thread and only applies to 10.9.2/Server 3.1.1.
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Alright, so I had 4 hours to kill on a saturday afternoon to figure out what should be possible in under 30 seconds with a few mouse clicks. If you're reading sarcasm with a dash of annoyance in there, good. Mission accomplished.
Firstly, delete the printer(s) you no longer want the normal way via System Preferences.
To get into the database via the Termainal:
sudo psql -U _devicemgr -d devicemgr_v2m0 -h /Library/Server/ProfileManager/Config/var/PostgreSQL
Once in list your printers with:
select * from printers;
Delete the one(s) you don't want with:
delete from printers where id=[put the ID# of the printer you want deleted here];
\q to exit when done.
Like I said, a couple hours this afternoon, I'll be testing it further to see if it breaks something else. 😝 When I went back to Profile Manager and chose to add one to a profile, sure enough the ones I no longer wanted were gone.
Love to know if this helps someone!
-Steve