The invoice you created a Credit Memo for is still linked to the Estimate.. because an invoice was created using that line on the estimate, QB will show you've invoiced that line.
To verify, the Estimate should have a little green check mark on the right of each line that's been invoiced. Check marks either indicate the line has been invoiced or it has been manually closed out. On the Invoice you Credit Memo'd, look at the right of each line - there should be a little chain link image, and clicking on it will display the Estimate that line is linked to. This link needs broken.
Try deleting the line(s) from the Invoice you CM'd. Click the little trash can image on the right of the line(s). You might get a popup asking if you want to remove the line or unlink it. The Unlink option might work, but I know Removing Line will. This will break the link between the Invoice and the Estimate. Re-enter the same information that was previously on the Invoice, manually (if it's a lot of lines/info you can copy/paste each line or, if it's not really important, shortcut this by creating 1 line with a short memo and the total amount. The CM is applied to the entire Invoice so it doesn't matter what's changed on the Invoice as long as the total amount stays the same). Because you're manually entering the information instead of "copying from Estimate", nothing will be linked to the Estimate. Click Save and Close.
You can verify the link was broken by going back into the Estimate to see if there's still a little green check on the right of that line. It might still be checked because QB might have it recorded as "Closed" (which is ok if you don't want to do anything else with that line.. I'd uncheck it just to be sure everything's working). Unfortunately you can't just uncheck the box to begin with, you have to unlink the lines first.
The Estimate should now show that line as Open and hasn't been invoiced. The Estimate will only reference Invoices that are generated from the Estimate, so you should only see the total of the other invoices on it.
If you want to invoice that line again in the future you can. If not, you can either leave that line open on the Estimate (no check mark), manually Close it (checking the box will Close it without adjusting any amounts, and stops it from showing up when creating Invoices from the Estimate), or adjust the Estimate so it reflects only what you want it to (for instance, delete the line entirely).
*OR* delete the invoice and credit memo and create journal entries so your overall financials remain the same. You can record Debit: A/R, Credit: Sales Income to record the invoice (dated last year), and Debit: Bad Debt Expense, Credit: A/R to record the cancellation of debt (or whichever account reflects why the invoice was CM'd, and dated whatever date the CM had). This option depends on what you need your books to show. If you sent the Customer the original invoice and credit memo, it'd be better to leave those on the books and use the first option so you have the exact same records they do.
