Re-running Payment run

Here is confusing and a challenging one for you.
We use the tcode F110  to pick up the to-be paid documents, create a proposal, and then run the payment for them.
We had 5 documents that were to be paid. Ran F110. Proposal worked fine. However 3 documents were cleared without corresponding checks, and the remaining two had checks against them.
We know why the checks were not created for 3 documents.
We used FBRA to reset the clearing documents( with no corresponding checks), and voided the other two checks using FCH8.
We then re-ran the same payment run, and this time it printed all the checks. But used the original clearing documents( ones that we had reset using either FBRA or FCH8). As a result, the original to-be paid 5 documents were not cleared against, and when we created a new payment run, these 5 documents were again picked up.
We had to do the same few months ago; the only difference was that we voided checks/reset the clearing documents, deleted the proposal from the original payment run and created a new payment run.
Any insight?

Hi Karthik,
The tables REGUH, REGUP and PAYR are only reflecting what we can see in the transactional screens .
My question is more business process issue. Clearing/voiding and then re-issuing should have triggered new clearing documents. And even if it uses the same old clearing documents, atleast the system should have cleared the open items.
So much so, although the checks have been issued, none of the accounts - G/L cash account and the subledger accounts have been posted to. So our cash account is overstated by the total check amount that has been issued.

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