We just ran into it too, and I'm pretty annoyed, especially I'm using Advanced Shopify.
HEY SHOPIFY!!!! Can we get a response please?!?! I run a custom furniture store with well over 20,000 sku (when you take all the variants into account). I would love to hear an explanation of why you think this limit is a good idea.
Why is this a problem you ask? For example, I just got a 7% surcharge from my largest builder, what used to take a day to update (in 999 chunk batches) will now take 4 days. Everything I sell before that's completed I will lose margin on.