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.