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You can remove the entire current contents of the resource database from the X server, using the -remove option.
There is no way to delete a single resource definition other than to read the current xrdb values into a file, remove the unwanted resource specifications from the file, and then load the file back into the resource database.
For example:
xrdb -query > filename
Use an editor to edit the file, deleting the resource definitions
you no longer want and save the file.
Then read the edited values back into the resource database:
xrdb -load filename
If you are running scosession, these changes to the resource database are stored and used again in future sessions. If you are not using scosession, however, these modifications are only implemented for the current Graphical Environment session. If you log out and log back in, the deleted resource definitions are once again loaded into the resource database. To remove a resource specification permanently without running scosession, you must edit the resource file that contains the definition.