A standard system restoration, either done by holding down the rightmost white key while powering up, or via the function. When performing a system reset there are a series of boxes that can be checked off so this can be selectively performed. However, in order to bring the keyboard to new, out of the box condition, all boxes must be checked. These include:
System Setup
MIDI setup
User effect
Music Finder
Files and folders
registrations
When a full factor restoration is executed, and all boxes are checked, all of the above are deleted. This is the case on every Yamaha arranger keyboard ever made.
Now, lets say that you did not place a check mark in the boxes for registrations and files & folders. If there were corrupt files in either of those areas that were causing problems, those corrupted files would remain in place and the problem would persist. If you backed up those files to a USB drive, the corrupt files would no longer exist in the keyboard after performing a full factory restoration, however, upon loading them into the keyboard from the USB drive, the problems they created just returned.
For the above reasons, I always recommend that instead of transferring all those registrations, files and folders to your new keyboard, why not just redo them from scratch using the new keyboard with all it's newer, updated features and sounds. Just makes good sense to this old codger.
Good luck,
Gary