Hi;
Carefully read brief, and had a look at the samples. One critical question: Files include some numbers like SKUs, serials, etc. Is that numbers have necessary fields on Woocommerce?
Also: are you on a manageable server? I'm asking this, because Wordpress has some so called "WP-cron", which is not a cron really, not reliable, and resource hog.
I worked with Woocommerce quite a lot, and replacing/adding even few thounds of records on a moderate server is not a performance issue - but wp-cron, its a bust. A proper Linux Cron is needed with a necessity like this. Work with me or not, I highly advice against using WP-cron - another idea is to fake a URL, and use some webservice to run it. Like, [login to view URL] I advice against that, too, as this will go through webserver, which will put too much stress on server with big updates. (Running a PHP script with Linux Cron is entirely different; its super fast and not resource intensive as it does not use webserver like Apache). Also, with a proper Cron daemon, its possible to load-balance, like running script with a lower priority, which wont ruin server performance)
Please feel free to ask questions you have.
Best regards,
Baris Atasoy