You archive a commission record when you want to remove it from display and being included in any of the site reporting. You can do this by updating the commission record to an 'achieved' status.
If you remove a commission record where there is an active commission rule, the refresh process to import the invoices will recreate the commission record. If you would like to hide the commission record and leave the commission rule in place, then you should 'archive' the commission record. Archived commission records are not visible to sales agents and will exclude the record from all reporting.