There's a difference between a project and the files that are attached to the project. If someone owns the project, they can download any of the files it contains at any time. If you upload a new version, they'll be able to download that too (unless you specify a separate price for that file).
Ah... there's a problem with that then...! I intend to put separate prices because:
1) I want a "demo", a free zip with 4 pages or so, so people can check if they like the beginning of the comic before buying it. So there would be two separate files, one free, another not free.
2) If I make more comics in the future, they'll be different issues/episodes of the same project, so they'll be in the same page. Each of them with the same price, but different... packages, so people would have to pay again for the next issue/episode.