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Which version of Bladelogic is this and are you running the DB Cleanup from NSH directly or from a Bladelogic script?
On 8.0 we had a problem that running the Cleanup from a BL job caused it to hang. The workaround was to redirect the output from the blcli call to a file or /dev/null.
As to how long it normally takes, that does depend on the amount of data to delete and how long ago the last cleanup was run. 12 hours sounds too long, esp. if you have run cleanup within the not too distant past.
We're running Version 8.0 SP 6. I'm trying to run the cleanup from nsh.
I think I made some progress by just waiting. It took over 12 hours for the job to finish but we finally got there. Future cleanups should be much faster. (It had been a while since our last cleanup)