Removing Old Vendor Invoices/Credit Memos

You'll want to write them off as bad debt, Txroofer.

Writing off a bad debt ensures your accounts receivable and net income stay up-to-date. This is when you're unable to collect the fees.

Let me show you how it works in QuickBooks Desktop:

Step 1: Add an expense account to track the bad debt

1. Click Lists on the menu.
2. Select Chart of Accounts.
3. Select the Account menu and then New.
4. Select Expense, then Continue.
5. Enter an Account Name, for example, Bad Debt.
6. Select Save and Close.

Step 2: Close out the unpaid invoices

1. Click Customers menu.
2. Select Receive Payments.
3. Enter the name of the customer in the Received from field.
4. For Payment amount, enter $0.00.
5. Select Discounts and credits.
6. In the Amount of Discount field, enter the amount you'd like to write off.
7. For Discount Account, select the account you added in step 1, and select Done.
8. Select Save and Close.

You'll want to run the  Accounts Receivable Aging Detail report after to check the customer's open balances.

Let me know if you need anything else.

I know this question is old, but perhaps I can provide a different scenario.  Back when I didn't realize what I was doing, I deleted vendor invoices that had payments already applied against that invoice.  QB doesn't understand when you do this, so guess what happens?  It is no longer applied as an expense, but it remains as a "floating credit" against your accounts payable.  So let's say your A/P on your balance sheet says your balance is $35,000.  Your "vendor bill" section says $40,000. But then you see on your Vendors List under "vendor center" a negative balance from a vendor for $5,000 from 3 years ago (let's say).  Well, it's negative 5,000 because you know for a fact you paid that vendor 3 years ago. When you click on that vendor info to see why the balance is (5,000) you realize that it has a "Bill Pmt" but there is NO BILL to offset that payment because it was DELETED.  You have to re-create that bill for whatever current tax year you are in, because you never actually expensed it the year you were supposed to!  And you can't create the bill for the year it actually belonged because it's too late, the taxes were already done and it wasn't actually accounted for.  

Create a Journal Entry for the current tax year, DEBIT the amount of the credit for whatever the expense was supposed to be,  then on the credit side, you will choose "Accounts Payable" and then make sure you apply it against the vendor it originally belonged to. Finally, you will go back to VENDOR PAY BILLS, now you will see the bill from the JE you just made, and you will "apply the credit" that had been floating.  Now that floating credit/negative balance will be gone and that reduces your income for the current year since you never actually used it the previous year.  

If you still see a difference with the balance sheet AP balance and the Vendor Bill Section, run a report on the AP in the balance sheet section for ALL dates and sort by VENDOR.  If you see vendors with negative balances, there is another solution to Re-create or create invoices for Payments previously made to those vendors.  

Attorney/Accountant for 15 years, using QB for 15 years.  Hope this helps and makes sense! PS: I use the accrual method.