use warnings;  # Great :)
use strict;    # Also great :)
...
        
        # Ok, so here you open the file for INPUT. Great :)
        open(my $fh, '<', $file) or die "Could not open file: $!";

        ...

            # Ok, so here you show the line to the user, mutatis mutandis.
            print $line;

       ...

       # But where did you open the file for OUTPUT?
       # And where did you write the line (changed when applicable) to the file?

    # This code is unnecessary.
    else {
        next;
    }
}