First of all I'm very sorry for the lost file. Let's get to the bottom of this so that doesn't happen again.
I'll try to summarize my understanding of the issues, please correct me if I'm wrong.
1. Your workflow is to record video pairs with two Sony DSC-H20 using the internal memory cards. Then you transfer the files manually to the computer. (No live capture).
2. You record a single master video for each camera.
3. For each camera master video, you then create several sub sequences. You do this using Kinovea, setting a working zone and saving it.
Issue 1: When reopening a pair of sub-sequences, the endpoint and duration do not match, although the original working zones matched.
4. For each pair of sub-sequence, you open the files in Kinovea, create a new working zone to fix the endpoint from issue 1.
5. You save the fixed-up sub-sequences again.
Issue 2: When saving one of the video, the other video file becomes corrupted.
Issue 3: QuickTime cannot open any video after it has passed through Kinovea saving.
Please correct any misunderstanding.
Let's also name things:
1. Creation of master files A and B in the cameras.
2. Creation of files A1, A2, …, A12, and B1, B2, …, B12 in Kinovea.
3. Creation of files A1fix, A2fix, etc. and B1fix, B2fix, etc. in Kinovea.
The major issue is #2, file corruption.
There is one critical bug that can cause this, it happens when you overwrite an open file. For example, if you open A12 and B12, fix A12 endpoint, then in the Save File dialog you either save it back to A12 or B12. Please create a backup of your files before attempting a reproduction of the issue.
I'll add the necessary check to prevent this failure.
edit: analysing the log, I think it is indeed what happened:
1673000 - DEBUG - [Main] - VideoReaderFFMpeg - [File] - Filename : Part11-030-Oil.MP4
...
1683468 - DEBUG - [Main] - VideoReaderFFMpeg - [File] - Filename : Part11-462-H2O.MP4
...
1802000 - DEBUG - [Saving] - FrameServerPlayer - Saving selection [1001]->[225225] to: Part11-030-Oil.MP4
...
1823468 - DEBUG - [Saving] - FrameServerPlayer - Saving selection [1001]->[238238] to: Part11-462-H2O.MP4