I made sure the thread was placed at approximately the same rank as the thread was before merging, using the re-upping system described at https://news.ycombinator.com/item?id=26998308.

That doesn't transfer the votes, but the re-upped submission is guaranteed to get extra upvotes because it's now on the front page, so I imagine it evens out in the long run.

(Eventually we'll implement some sort of karma-sharing system for submissions of the same story, but there are a lot of other things to get done first...)