The dealership isn't going to care what any logs show and the fact that you have logs may be sticking point that you modified the ECU. Generally speaking, they are going to want to see some very noticeable driveability symptom(s) before making any diagnosis for warranty repair.
Given the engine has been pulled and replaced, this really could be anything. The knock sensor may have been overtorqued when installed causing knock to be reported when none exists (false knock). You can also get false knock if something in the engine bay is rattling that is picked up by the knock sensor (like a loose heatshield). Given the history of the car, it could be that the motor is on its way out. It could also be some other mechanical issue (bad MAF, bad front o2, etc.).
Do you have any wide open throttle (WOT) runs in those logs (if so can you point out the row number)? I would not do any WOT runs at this point but if you have them already it would be good to take a look.