Sorry for the late reply.
Here is what I could find by debugging the process.
Codeunit 10320, ProcessDetails
The data get transfered to the Data Exch. Line Def and there is a COMMIT after the insert
Then the Codeunit 10327 is called, PrepareEFTDetails, and this function calls UpdateEFTExport from Codeunit 10098 where the Transmitted field gets set to true.
Same with 2nd line
Then I have an error on the 3rd line, but since there is a COMMIT before, the first 2 lines are still flagged as transmitted
The user corrects the error and click on Generate EFT Files again, and the first 2 lines don't appear in the worksheet, since they were flagged as transmitted