Its not going to charge instantly.
You can try to let it be for a few hours.
Its possible that it will be fine, possible you will see a noticable drop in battery life, or possible it wont even hold more then a 5-10 min charge.
Those warnings are there for a reason, if the pc shuts off due to being at 5% you should never repower the computer without plugging it in first. If you did not keep turning it back on then the system must have frozzen or windows updates run and when it rebooted and applied updates is when it went critical