If you have to do this task in stages (and there's a couple of suggestions here to improve the way you do things in a single pass), don't hold the csv file in $_SESSION... that's pointless overhead, because you already have the csv file on disk anyway, and it's just adding a lot of serialization/unserialization overhead to the process as the session data is written.
You're processing the CSV records one at a time, so keep a count of how many you've successfully processed in $_SESSION. If the script times out or barfs, then restart and read how many you've already processed so you know where in the file to restart.
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