Yes you can delete it from ePO master repository but Extra DAT file can't be remove from ePO console on local machine. It can be replaced by new extra dat file but you can't delete.
Best option is remove locally extra dat file on machine and restart the system. But if will OK for few machines not for all the clients.
Additionally, extra dats have an expiry date: once the signature they contain is included in the main dat, the extra dat is no longer used even though it's still present.
The best and quick way is to create a pup (Unwanted program) user detection for Extra.dat. Then do a Scan in the Engine McAfee folder and the extraDAT will be detected and deleted