So I checked everything, the notifications only indicate that there has been a successful firmware update in the meantime.
What, between you upgrading the software and your data going missing? Is Firmware Auto-Update enabled (it might have been enabled when you did the system restore…)
I note that a firmware upgrade was announced yesterday; is this the version you now have installed?
Interestingly, my MyCloud is only telling me that there’s a 4-01-02-417 upgrade available…