Did you upload the new content with the “Set a different price for this file” option?
If so, then from my understanding, every user would have to pay $2 regardless if they already own the project or not.
Personally I would suggest against asking current owners of your product to pay more for updates. This gives them the message that your product is not one that they buy once and that’s it, but that they will have to keep investing into it. This is especially troublesome if your project is not in a stable state yet, and customers are buying it anyway, to help fund it to completion.
If you really want to change the price of a project, I’d suggest you change the “Minimum Price” under “Edit Game”. People owning your project won’t have to pay for the updates, but new people will now have to pay the new price to gain access to it.
To me it sounds like some of your users paid $2 (basically donated $1 more) so they can help your project, and suddenly they are being asked to pay $2 more to receive the updates they funded.