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It depends on what version of Protect you're using. In 7.8 and later versions you can go to Tools > Database Maintenance and use the built in maintenance tool to clean out old results. In earlier versions (7.6 and below) you have to delete results through Manage > Items.
I'm using 8.0.0, I have the maintenance tool, but I only have options for Patches(Deployment), Assets, ITScripts, and it works for those 3 things, but not Patch Scans. Right now I'm manually deleting from Manage > Items. If I select too many to delete it will fail and kill the software. I have to reopen and try deleting a lesser amount. My current database size is almost 60GB.
The 'Patch' option is meant to delete both patch scan and deployment results. It sounds like you may have more complicated issues, and I'd recommend you get in contact with support directly. I'll be glad to help you work on this - if you email or call you can ask for me.