I'm not entirely sure what you are trying to achieve, but the issue seems to be that you are only locking the file open not the file writes.

 so :-
fork 1                      fork 2

takes the lock
opens file1
releases the lock
starts writing data
gets pre-empted
                            takes the lock
                            opens file1 (& deletes contents)
                            releases the lock
                            starts writing data 

Etc....
[download]

So potentially many children all writing to the same file at the same time. If you get each fork to write a different character to the file you'll see what's happening.

It's usually better to get each child to write to its own temp file, File::Temp, then rename it.