Moving the check for $read == 0 was quite appropriate. Admittedly, $skip was not optimally named. (I'd prefer $in_bad_record. It was called $skip because I initially discarded the bad stuff. I didn't notice you wanted to keep it.) However, your fix of the bug in read wasn't optimal.
Me:
my $read = read($fh_in, $buf, $blk_size, length($ofs));
You:
my $read = read($fh_in, $newbuf, $blk_size);
...
$buf .= $newbuf;
What it should be:
my $read = read($fh_in, $buf, $blk_size, length($buf));
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