If by "overpaid" you mean there is a line on the Vendor's Invoices list with a negative balance, you'd just do a manual payment to offset the negative balance with the invoices you want to apply that to.

Enter a check # starting with APP to do this kind of zero $ manual payment.

No we sent them a check based what is in Sage so the balance shows as zero

Then Sage 100 data doesn't consider them overpaid.

If you sent a check from Sage AP, and that "paid an invoice in full", with a now zero balance; then how did you "over pay them"?  

They have undistributed funds on our account with them.
I asked them for a list of all open invoices and everything is square.

So on our end we somewhere made an error with data entry but we do so much business with them it would take too long to determine which invoices were entered incorrectly.

That is exactly what you have to do: validate entered data with reality.  The system can't identify incorrect data entry for you.

When you find the problem, we can advise on the kind of transaction to use for correcting the system, but you need to find the problem first.

Thankfully they were able to narrow it down to 1 check. 

Is it possible to only do a partial check reversal so that the invoices that were paid from that check stay marked as paid?

Or do I need to do a full reversal and then do a manual check with the check number?

I don't think Sage will allow a partial reversal.  Basically, when you enter the invoice # it asks if it's a reversal and whether you want to recall invoices.  Whether you can edit the created transaction after those answers, before posting, is something you can try in a test company.

Thanks. I think it will look cleaner just to do a normal check reversal and then just redo the check,

Thank you for your help