If your game is pay what you want and you have those misleadingly named individually priced files or not, has no bearing on this. Your project is in the purchased library of anyone giving you more than 0 or having it claimed in a special sale with claiming enabled. If you change the project minimum to 1 or 100 does not matter. Any normal projects files will be downloadable.
The "individual file pricing" mechanic causes a lot of misunderstandings. It is meant for bonus items. But that would be dlc. And dlc is something I expect to buy on top after I have bought the game and was happy.
Anyone paying for your project is at a payment level. Any files below that level are downloadable. And the problem arises, when you have more than 1 level of bonus content. Like 0, 5 and 10. Someone bought level 5 and wants level 10. It is not possible to raise the level! Buying the game again will give you 2 keys with level 5.
It gets more complicated with sales and even more complicated with bundles. I am not sure how those are handled. Oh, and bundles can have a bundle discount on top. I assumed that discounts would be factored in to the individually prices files somehow. But I am far from sure, it could also be a an unmutable check of factual payment, instead of sale-adjusted payment.
Oh, and the name alone gets people confused, hence your customer that asked about paying again. English is not my native language. While I boast to be fluent, even I would actually assume that something named individually priced files would indicate that those files are not attached to the project and would be sold individually, like the name says. Maybe what the feature does was changed, but the name stayed. Or there is some context I miss.