Hello Sandip,
It sounds like there may have been a posting interruption while posting the payment, and the apply record is there, but the payment itself may be missing from some tables. Check links will do different things based on if the PM keys record (PM00400) and transaction detail record (PM30200) are there or not. Did you run check links on the Purchasing series for the 'Transaction historical files' option? (If not, do this in a Test company first as check links is non-reversible.
If it doesn't help, you have various option on the data-fixing needed to fix it in GP.
Option 1 - You can use the 'remove transaction history' utility to remove the invoices too from history, and then rekey it all back in brand new again. Do not hit GL again when you rekey the invoices and payment back in. (This would be the supported method - to remove and rekey.)
Option 2 - If you can view the payment to VOID it, try that, but you may run into errors if the payment is damaged. But voiding it would move the invoices back to open, so you could rekey the payment back in and reapply it to the same invoices again. (This may or may not be an option for you.)
Option 3 - If you are good at SQL, you can look for information for the payment on the other records present in the SQL Tables (PM00400, PM10200, PM10201, PM20100, PM30300) and use that information to insert the missing record for the transaction back into the PM30200 table. (This would require an 'insert' statement, so is not supported, so you would be on your own to do that if you know how to do that on your own.)
If you need any help with this issue, it may be best to open a support case to get assistance from a support engineer or your Microsoft Partner.
https://serviceshub.microsoft.com/supportforbusiness
Thank you in advance,
Cheryl W
Microsoft Dynamics GP Support
