That's never the goal with securing a system, though. The goal is to mitigate risk to a level acceptable to the various stakeholders involved based on what said stakeholders value.

Including paper ballots?

Some systems that use paper ballots photograph each ballot before it is counted. This helps with auditing counts later on since every count must exactly match.

Paper can easily get 'lost' or 'replaced.'

The advantage of paper is it's bulky so it's hard to swap out if people from multiple parties and observers etc are paying attention.

PS: Remember the oldies, "Vote early, Vote Often" and "It's Not the People Who Vote That Count, it's the people that count the Vote"

Preventing "lost or replaced" with paper ballots is a straightforward exercise in good human process. There are states that do not have good human process to manage their ballots, despite the example of other states that do have good process. Those states are incompetent/malicious.