Once I was doing a run and managed to reach the Flagship, it hacked my weapons, but suddenly the electricity where I live went off for like half a hour, when I came back to at least finish the run (Without recording) I noticed I was in the start of the fight and now the Flagship hacked other system, I don't know if it's something known and neither how to replicate it, but I'm making this post because maybe it could be used for consistency in beginners run when Weapons Shields etc is hacked. Thanks in advance :)

the game probably sees a reboot like that as a fresh entry to the fight. Could maybe try alt-f4ing before the drone connects to see if that prevents the auto save. I know in Hard No Pause its generally best wait at the base for the flagship so you jump away and back in to reroll a bad hack