Flashing doesn't void your warranty, they are just not under any obligation to help you with support questions if you flash your device to something other than the proper versions sold with the phone, so running US firmware on non-us phone for example. Yes they are allowed to charge you to get your firmware back into a state that they can provide support, as you flashing to a non-supported firmware for your phone is not covered by warranty(but it doesn't void your warranty completely)

now to understand your problems

After reflashing the firmware and formatting the eMMC,did you try to use it in this state after this, and before restoring a backup? If yes, did it have the same problem?

Also, do you have a microsd card in the phone? if yes, have you tried removing the battery and the microsd card, and then replace only the battery, leaving out the microsd card, and reboot and see if you still have any problem?