When someone pays for your game, they gain access to all files available in that project indefinitely. That means if you upload a new file, and delete the older one, users will be able to access it. The only exception to this, is if you’ve set a different price to a specific file, but I’m not sure what happens if that file is then removed.
One way to make updating easier, is to use the Itch’s tool “butler”. This allows you to upload a project, and also update it on the same file, while also keeping all older versions available in the Itch app. Also users using the app will be able to update their game without re-downloading the whole project, as “butler” knows how to update only files that need updating.
More information can be found on Itch - Introduction - The butler manual