Haven’t tried it, since I only sync with my PC and cloud server. But I just checked up and Librera has an option to save progress and profiles to a custom directory, so I guess that would be the way.

These are the ones I actively use with syncthing

• Markor - for quick note taking and todo’s
• Librera reader - ebook reader
• Seeneva - smart comic reader
• Voice - Audiobook player
• Simple music player
• KeeepassDx - also