Is there some internal command to do this? Sometime need it to clear the Everything collection.
You can delete the collection itself:
e.g. Delete coll://Everything
If you need it to exist afterwards, you can recreate it:
e.g. CreateFolder coll://Everything
(You may not need to re-create it if the thing that outputs to it does that itself when needed.)
As an alternative, DOpusRT.exe has a /col clear command which you can use to do similar (including from outside of Opus): External Manipulation of File Collections.