The system addin Link makes, uppon connecting to USB, a folder called SAVE-F that holds a copy of all files in the MCS.

Oh really? Reading the manual would have told you this (or better, that you are wrong). And SAVE-F only saves the "rejects", i.e. the files that couldn't have been transferred from @MainMem to the MCS after disconnecting USB.

@MainMem is the folder to which all the MCS is put when USB is connected. It is not the main memory, just a converted-to-g3m mirror that is made when you start a USB connection!. When USB is disconnected, the OS transfers everything from the @MainMem folder to the actual MCS, converting from g3m (and txt, for programs) to main memory files. The files that can not be converted are saved in SAVE-F. This is explained in the manual, why don't people RTFM?

The @MainMem folder is not touched otherwise and stays in the SMEM; it is hidden by the OS on the native file browsers (but can be shown using our own file browsers - I chose to hide it on my file browser library).

I repeat, the @MainMem folder in SMEM is not a way to access the MCS, at least not its current state at any time. It is just a folder that is created by the OS to let the user manipulate the MCS on a USB connection.