I want RefWorks to re-use the RefID numbers that had been used by the 2000 references I just deleted. How can I make it re-use these RefID numbers?

You cannot make RefWorks reuse the RefID numbers that had been used for references that have now been deleted.

In fact, it's important that these numbers NOT be re-used. Ref ID numbers are the primary way RefWorks identifies the citations you wish to insert in your documents. Let's say you insert a citation for the reference with RefID 6000 in a paper. Let's further suppose that, while using RefWorks to check for duplicates, you delete the reference with RefID 6000 by mistake. Because RefWorks doesn't reuse RefID's, when you format your paper, you will be told that RefID 6000 doesn't exist. You will be able to look at the code for RefID 6000 to determine what reference you wished to insert, and you will be able to fix the problem by citing the new record for the reference or by restoring RefID 6000 from the "Deleted References" location. If RefWorks reused RefID's, Ref ID 6000 might have been assigned to a new reference and that incorrect citation/reference would have been inserted in your paper.

If you want to start an account from scratch (starting with RefID 1), you can create a new account and import the records into that account. However, you will never be able to get an account that re-uses the RefID's for deleted references. (Other bibliographic management programs have this same prohibition on re-using the automatically assigned numbers).