Pumping it back into wells as oil is maybe a good idea. If civilization completely collapses back to the Stone Age humanity might never rebuild and advance into an industrial era if there are no more easily accessible fossil fuels. The rapid advancements of humanity of the last two centuries is because of fossil fuels. Of course there is a chance future humans after the apocalypse can advance without fossil fuels. But we don’t know for sure. To give them a fighting chance we have to replenish whatever we took out of the ground. Otherwise they might never advance past a medieval era.

Another idea is to bury tree logs into old mines where it can’t rot so it will fossilize into coal over centuries.