Code for new flooring over gas lines
That pipe is already left open and surely not active or charged. Cutting it again will not be a problem, since it is no more than cutting it again slightly lower than what it is already.
If you want to go the safest route, since the floor is being redone anyway, remove enough of the existing floor to cut it below the existing floor to place a self sealing cap over it like Sharkbite (r) or similar brands. Please note, to do this the cut needs to be cleanly done, in order for the seal to be effective.