The game has no problems at the moment.
There are about 500 files in a single folder and everything runs fine with that.
If we implemented saving with Sams Journey Loader, there would be the problem you describe. (about 300 files would be missing in the later game).
The Sams Journey Loader can only access 256 files. No matter if on a disk image or in a folder. It uses hexadecimal numbers for the file names like "1a", "ff", "ea" and so on. But these can only go from 0-255. So with Sams Journey Loader, only 256 files would be possible on the disc or in the folder.
We do not currently use the Sams Journey Loader. If we were to use it, we would run into problems. So saving is not possible at the moment. There is nothing we can do about that.
It is not a question of "file version" or "disk image" version.
If Krill's loader is ported (implemented in SD2IEC firmware) one day and supports saving, I may try the whole thing again with this loader (Krill's loader).
If you decide to use a loader system, the whole SD2IEC will stay in that mode (until a "reset" is done). There is not yet a widely supported (and fast) loader system that supports saving.
As I said, this feature is currently stopped. I will update this page here when there is news. There is nothing I can do about that. Saving to SD2IEC when using an IRQ loader has been a major problem for almost everyone out there for "ages". The forums are full of complaints about it and nobody knows a solution except to update the firmware with a custom patch.
You can write to "st dot mader at gmx de", I don't think it makes much sense to communicate about it here. The topic is too complex...