My File::Edit::Portable was written to deal with this exact situation.

Get a file handle of the file with the record separators changed to that of the local platform, make changes, and write it back to the same file with the original record separators:

    use File::Edit::Portable;

    my $rw = File::Edit::Portable->new;

    my $fh = $rw->read('file.txt');
    ...
    $rw->write(contents => $fh);
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Get an array of a file's contents with the line endings stripped off (one line per element), make changes, and write the data back to the original file (the original line endings will be preserved and put back into place automagically):

    my @contents = $rw->read('file.txt');

    for (@contents) {
        ...
    }
    
    $rw->write(contents => \@contents);
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There's a myriad of other magic you can do as well, like automatically making a backup copy of each file, chaging line endings, using custom line endings, checking what endings a file is using, splicing stuff into the files etc.