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You're on the right track. The file size or amount of lines should not matter, imho.

The sed command you mentioned will not work. Here's a fix:
sed "s/\(.\{4031\}\)......./\1/" $filename >...

I'm afraid above will not work as you lost inportant chars. Try sed "s/\(.\{4031\}\)......./\1/"

That should work as you apply the command to only one line at a time.

Although both sed and cut work on Ubuntu, the standards only require sed to work on text files. Files with lines containing more than 2048 bytes are not text files on HP-UX. The cut utility,...

Similar questions have already been asked and answered here. Right at the bottom on this thread you'll find these threads.

Check...

If you are using bash, there is no need to call any external tools to perform this. You can use parameter expansion alone as per below:

# Example line variable
line="this is an example line of...

Try:
cut -c -2,4- file