There is a kb 222924250018024 which explains how to get rid of the message that invoice is already paid.  The kb has instructions for earlier versions as well. 

Warning: This procedure clears all check data entry information and resets the Paid Today flag. Use this procedure only if restarting check payment selection from the beginning is not a problem.

1. Make sure users are out of the following AP tasks:
   • Invoice Data Entry
   • Check and Electronic Payment Maintenance
   • Manual Check and Payment Entry.
2. In the Sage 100 Launcher, click File and select Run
3. In the Program box, type *utl and click OK
4. The "A/P Open Invoice Payments Today Utility" will be highlighted. Click OK
5. Click Proceed on the warning message, "This utility verifies that the Paid Today field is set correctly in the Accounts Payable Open Invoice file. Important: Before running this utility, everyone must exit Invoice Data Entry, Check and Electronic Payment Maintenance and Manual Check and Payment Entry."
6. The program will run quickly and return you to the AP Menu
7. Verify that the invoice(s) is now available

Thank you Linda!