Flashing firmware does not wipe the hdd.
As regards switching SD off first, I suggested that previously but you were hesitant to try it.
All I can say is that it would make sense to me if the box defaulted to hd & sd both on after a reset because that would allow people without hdmi to access the box via component if there was an issue. But who knows?
At the moment you have a box that you can at least watch the recordings, perhaps wait until you have watched everything and then try all options.
If it was me I would have tried every option including a full reformat by now because I would hazard a guess that 90% of everything you have recorded can be accessed via the various catchup services (take some photos on your phone or write a list of everything to remind you).
Sometimes, like any computerised device, the box can get itself in a complete mess that only a full reset will cure. And then, sometimes, components fail in strange ways.