Triathlon mode without swimming - Fit file got corrupted.

AA triathlon I did got the swimming cancelled, so when using the triathlon mode, I just quickly pressed the button over swimming and transition 1, paused it and then restarted on the bike. I don't know if this caused something weird to happen to the file because now the activity wont sync with garmin connect and when manually uploading it says the file is invalid. I tried a couple of the free .Fit repair tools online without much luck. Fitfilerepairtool managed to fix some of it but left the running leg HR/GPS data incomplete on purpose unless I buy a license for $50. Any other options out there? Has anyone had the same problem before?

Thanks,