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One tip (I use this method) is to save different Project files when you do different tasks - this means you can re-load different versions. The Project will also save your actor settings and (if you've done any post processing) that'll save too - along with teh parameters you've set for trajectory filtering.
I'd suggest starting a clean project. Load your calib/actor files and start from scratch. This way, there's no project cache. Also, so it's easy to manage your data, keep the filename of teh video but add characters (so it's easy to identify).
Then, when you've done a track you're happy with, mark the ROI's and save it. I always save one like this, I add 'xxx_RAW' to it's filename, so I know that it's not been worked on (ie this version does not have post processing applied). I use RAW and POST in caps so I can easily identify the project file, handy when you're scanning through lots of shots :)
I then save another copy, with 'xxx_POST' added to the filename (this is a copy of the same data, but, as it has a different filename it's a different cache/project etc). Now, mess about with this one and apply filtering etc. When you're happy, save this. It'll write over your other version, but that's OK, as you now have a RAW and a POST version.
The advantage with this method is you can always load a pre or post version. Obviously, you can do more work on the file, just make sure that, before you do, you save another version (ie WIP_01) etc as, if you don't do a save before you start, the project file will be updated/changed.
That's probably what happened to your data, the project file has been worked on too much, that's why a fresh start might help (unless you've tried that already?).
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