Thank you for the responses!
Sung also reached out and had similar thoughts, including that it is probably not wise to mark virgin queens.
One of the things I've gathered is that it would have been better to either leave both queens as-is, or to move the mated queen to a nuc. My first instinct was to leave both queens in the hive, but then I realized I could potentially get a new hive started, which I was planning to do later in the season anyway. If I had instead moved the mated queen, I could always recombine with the original colony if the virgin didn't successfully mate.
When encountering new situations in the apiary it can be difficult to know the right direction to take, and decisions need to be made quickly. Having a good rule of thumb or standard process could help to make timely decisions in certain scenarios. Would this be a good one, and would there be scenarios in which it doesn't work?
"When queen cells or virgin queens are found in a hive with a mated queen, move the mated queen to a new hive."
This covers both the situation described in this thread (a likely supersedure) and the preemptive swarm control process described by Wally Shaw.
Cheers!
Thom