Project damaged by updates

I have a problem. I recently uninstalled Pro CS4, reinstalled it, downloaded the latest updates. Now a project in the timeline is damaged. About half of the clips in the timeline now start and stop at the wrong point, their in/out points have been changed by a random amount, though all the clips are the correct length and the transitions all occur at the right points. I have two harddrives with the clips distributed between both, many are duplicated in both HDs. When I first tried to open the project after updating, no picture appeared in the monitor, it said Media Off Line. I managed to find the clips by looking in various places, but as I said half the clips now start and stop at the wrong frame. These faults are the same in all saved versions of the project, and also in the auto-saved versions. To repair all these faults would be a helluva job, especialy because some of the clips I chopped up into many small pieces, removing a frame here and there, changing the speed of some pieces, to smooth out jerky pan shots.
What has happened? and is there any way I can restore the clips to their correct start/stop points?
I didn't rename any of the clips or alter them in any way, except to use a few of them in another project (which is undamaged)
Has anyone any ideas?

Charles,
Not directly related to the OP's problem and not even applicable to PrPro, but in my decades with PS, I never had to "trash my Prefs," and felt pretty good about this. One day, while working on a rather large graphic, Java started to download an update. I had missed shutting this function down - my bad. Halfway through, it killed PS, destroyed my image file (luckily a Copy with few edits done). I had not touched the machine from the moment that Java started doing its thing. I watched in horror, as PS crashed. This had never happened in all those years. I restarted PS when Java was done and it was hosed! Trashing the Prefs fixed it, but that image (on the HDD) was also hosed. Guess whose auto update got "fixed" instantly. Unrelated coincidence? I do not know.
Going back, I was installing an NLE update (not Adobe), and Logitech's Set-Point started an update. I'd missed shutting that one off too. Not only did my installation get whacked, but XP-Pro was butchered, my LAN was disabled, System Restore would not work. Norton Ghost could not save my bacon. Nothing worked! Set-Point is history. My wireless mouse works fine without it. It took a low-level format and complete reinstall to get me up and running. This was on a brand new workstation with minimal apps installed yet.
Do these have anything to do with the OP's issue? Probably do not. Do they have anything to do with my shutting down all auto updates? Absolutely.
Hunt

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