Remember, downloading products is cheap... 100,000 products (minimum 100,000 SKU's) is 400 API calls. You can do that in one fell swoop.
Now you have the CPU cycles to be smart and figure out what to do. If you only update 10 SKU's, you have done nothing amazing but search for 10 things in 100,000. Big Whoop as they say. I got over the inefficiencies long ago... worrying about them gets you nowhere. There are too many ways this whole system (Internet cloud computing) is scotch tape and super glue for me to lose any sleep on it.
I believe you will be best served here by biting the bullet and recognizing that there is no shortcut to this. Believe it or not. You cannot cut corners and magically use a string with no real meaning in Shopify (SKU) to find variant ID's in order to update them.