It is resource-intensive yet viable to track every paper ballot throughout the process. Digital ballots have no such guarantees.
The best option to me seems to be scanned paper ballots, which offers the ability to perform analog recounts when there is suspicion of problems with the digital count.
(Disclaimer: only a distant observer of this, there may be better options.)
For context like 2018 congressional elections, or 2020 elections, what does it mean to track down paper ballots, such as to make sure the final count is complete? At least it sounds like de-anonymizing votes.
Or does it mean it's so logistically unpalatable that you can bet on it not happening? Same thing with recount as a remedy to detected anamoly; it's theoretically possible. But is it so unpalatable that a gambler may gamble well on an event?