In Colorado, ballots have unique bar codes for auditing purposes to ensure that the same ballot is not counted more than once. Some activists have concocted a conspiracy where it might be possible for an insider to correlate those bar codes with the names of the voters (I think this could only be done for write in or absentee ballots, but not even sure those could be matched to voters) and then use that information for nefarious purposes.
County clerks are on record that such activities would be illegal and seriously prosecuted.
The example given by those activitists in the lawsuit is a boss could coerce her employees into giving her the unique bar codes on each of the employee ballots. Then the boss could coerce someone inside the county clerk's office into giving her how those ballots were actually cast. So if that is their best example, pretty far fetched.
If you are truly concerned, then vote in person. It's been awhile, but I don't believe they record your unique bar code with your name.
It is my opinion that there should be identifiers to make sure each ballot is only counted once, but not one that would allow that identifier to be linked to a specific voter.
"Remember to always be yourself. Unless you can be batman. Then always be batman." Unknown