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.