Those are used (I imagine) for some of the reports that also come by default.
If you don't need any of those values, then yes, you can delete them.
You can always do a backup (export) and import them back if you need them.
I'm not using extraction, can you look up the data source of the reports? you may be able to modify its criteria to meet your needs.
I do not know more about it, I hope you find a solution.
Hope get answer
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CD-xxx is referring to CUSTOM DEFINITION usually (i.e. "things that you / your colleagues built themselves") ... not "Custom Data".
Custom definitions are built by following the process here -- How To: Create a Custom Vulnerability Definition in Patch and Compliance Manager -- ... the inventory data on (for instance) IE-versions shouldn't be used in those patch reports in XTraction.
This should be a case of apples & oranges - the two don't really have much to do with each other (though I can see how that might be the case).
You may want to review the custom definitions that your Core has (hint - it'll help if you filter by type in the console)...