Did you capture these files yourself? If you used live capture now to import into FCP and then later changed the file names in the project, the clip names in your scratch disks will not change to what you've labeled. If you capture files in the future, it's always good workflow to log and capture, naming each clip then exactly what you want so you won't have to worry about reconnecting to the wrong files.
This won't help you solve your problem quickly, but I would suggest that you close your current project. Make sure your scratch disks are connected, then open the last autosave file from yesterday. Reconnect the media files very carefully, making sure each one is the correct file. FCP notifies you that the clip media start and end has changed when you've not reconnected it to the right one.
Thank you for trying to help. These file were imported by log and capture and were atomaticaly converted to prores 422 LT. I did not mess around with file names, as the names were given during the log and transfer proccess.
This is definetely a final cut bug.
The problem dissapeared (not solved though, as the reasons remain unknown) with the folowing way:
a) I open one of the backed up files and looked at my rough cut wich consists of sequencies.
b) By playing the 2 specific sequencies on the rough cut, there was no error in the edit.
c) By opening these 2 sequencies on the project browser, there was a different edit !!!!
d) By going back to the rough cut and double clicking on the nested sequence, I could see the original edit.
e) Now I had one specific sequence in the timeline, the same name, the identical sequence, opened in two different tabs. In one tab (the sequence that i entered to through the rough cut) the edit was the original, in the other tab (the one that i opened through the project browser) the edit was distorted !!!
f) I copied the clips of the original edit to a newly created sequence.
g) I deleted the old- problematic sequence
h) i repeated the process with the second sequence that was altered by final cut on its own will.
I hope this will help someone in a similar situation and I keep this question as unsolved, because in reality noone really knows - until now- the reason for this situation. Thank god it was solved.