Writing a live USB with persistence from Windows

I’m creating a new project and am trying to decide on a platform where it should operate from. I’ve just started to play with Fedora and there is A LOT to like, but I still need to verify it fits my needs. Here’s what I want:

The project will be distributed to not-so-technical users as a downloadable ISO file. I’ll create the ISO from the base Fedora system, add in some apps I’ve written and create an ISO from that. I want the users to be able to write this ISO to a USB and run it live without needing to install it onto their computer. The problem is there is some data that needs to persist between runs.

I’ve seen that I can create a persistent USB by writing to the USB with livecd-iso-to-disk. However, this won’t work for my users who will be doing the writing from Windows and will probably be using something like Rufus. Rufus CAN create a persistent area but I believe that Fedora won’t see or use it.

Is there some way I can accomplish this?