When you logged into Windows, did it have prompt to run any updates? It's possible that this caused some changes in the BIOS and messed with the bootloader. Also, are you able to boot again into Windows at this time?
And, while booting into the live USB drive are you able to run efibootmgr manually from the terminal?
I would also suggest checking out this thread. Unfortunately, not two cases seem to be the same when it comes to this type of errors, and it's tough to point to one particular issue: