I have the exact same issue.

The phone battery was drain (due to old phone, nothing unexpected.)
I start the flasher and having a hard time relocating the .bin image to a specific folder to get access to it from the flasher.

My intention was as u can understand to charge the drain battery with the flasher.

What I did not know was that the phone had charged during the time of
relocating that .bin file.
I start the flash sequence, and HOLY **** the battery is at 17%, the process keep going.
Try to stop it as fast as i can.
But no.

Now it seems it wont flash any firmware I try.