Would it be faster to do relative seeks? I'm just thinking that toward the end of the file you're seeking across 300+GBs of data every time you delete a single line. would 
seek $fhRead, $r2 - $w2, 1;

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work?

Just a thought...

Edit: While it's obvious, i think it's also worth noting that if each record is the same size (which seems likely) then it can be done in one pass instead of two (or at least, one pass for each chunk of kill file, depending on kill file size).

In reply to Re^2: 15 billion row text file and row deletes - Best Practice? by jynx
in thread 15 billion row text file and row deletes - Best Practice? by awohld

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