My ecommerce site uses URL segments for faceted navigation, like so: example.com/shop/shirts/mens/purple/large
Recently I setup a process for updating the website's inventory from our internal system, so a bunch of products have become no longer available. It's caused many URLs that Google had indexed to become 404 because, using the example URL above - we no longer have any men's large purple shirts. There are about 2000 of them.
I hate to see all these errors in the webmaster account, but it is accurate. Is there anything I should do? Is my site being penalized for a sudden spike in 404s? I feel strongly that Google would push my site lower on the SERPs due to a sudden spike in 404s, certainly it must appear like an unstable or poor quality site. I considered adding those URLs to my robots.txt as disallowed, then requesting their removal... but what if I get new merchandise with those same facets? How is something like this usually handled in ecommerce?
Thanks for reading, I certainly appreciate your expertise.