If you have 1000 Products, and you want to update all of them, using the API, then you need to ask for all 1000 of your products. Since the API will give you them 250 at a time, that means 4 API calls. Since you are allowed 500 in 300 seconds, the 4 calls not stress the API too much. Once you get a block of 250 products you can update them one at time by looping through them and updating the field(s) you are interested in.
There are probably a dozen simple patterns to apply here. For example, you could read in your own custom CSV and for each Product in your CSV, ask the API for the Product and update it. This would be terribly inefficient API wise as you'd do 1000 calls, but hey, calls are free so who cares right.
You could ask Shopify for blocks of 250 at time, and then look inside the CSV file for matches. That way, you update up to 250 products with one API call, and a simple look through the CSV for the matches.
So... rest assured, no matter how you slice it, your request is possible to do, pretty easily, with basic scripting and the API. If you want someone to set you up with all the code to do that, just ask. I am sure there are plenty of coders that would take the time to script you a solution.