With all due respect, deleting the CM doesn't make any sense. Why issue a CM, then later go back and delete it?  

Here is how I resolved this problem.

1. Go to the Credit Memo issued to the account in questions and open it. 

2. Example:  Account, ABC Tool shows a -$500.00 amount remaining.  The work is complete, so it's time to issue a refund to ABC Tool.

3. Directly under, "Help", "Docs" is "Use credit to give refund".  Open it.

4. A "Issue a Refund" box will open.  Fill in the specific information.  Type the check number in the memo box, hit the "ok" button and done.  Check issued and account is at zero. 

Hope this helps!