but as I removed one drive, hdtoolbox asked me to update the RDB because the other drive was not present anymore, so I did.
I think this is where your problem most likely occured. How important is the lost data? If I were you, I would reinstall everything and make sure that I have the latest PowerFlyer drivers (contact Elbox support for it).
Another possibility (try this first) is that somehow your PowerFlyer config files got corrupted, and in that case delete everything from your ENV: which is PowerFlyer related, remove the Startup-Sequence PowerFlyer lines, and reinstall the PowerFlyer setup software. Afterwards, while rebooting hold the left mouse button in order to get to the early ATA3Prefs menu. Change from Split to No Split there. If you can't (ghosted option) let the system boot and then change it from within OS3.9 and click Save, then reboot again, and all should be fine.
Of course, if the Hard Drive won't listen at all if connected to PowerFlyer, your best bet is to back it up fully, without it being connected to PowerFlyer (only the on-board Amiga IDE interface), then reformat it, connect it to PowerFlyer, and fix the messed up/corrupted RDB. You may need a 2.5 -> 3.5" converter for this though.