You don't say how the battery is fitted. It could be fitted into the tube using a rubber plug or, in a Di2 specific seatpost using circlips.
Either way, only a klutz would make it go up the tube instead of down. Keep a longnose pliers handy, you may have to tug it a bit, but it all depends on how it is fitted and how deep it is shoved in.
As for e-tube - you won't need it unless the previous battery died by spiking the system and killing the flash memory. Then you'll have other problems.
Replace, go for a ride and drink a beer.