When a merge happens, the accepted answer of the target will remain accepted and the accepted answer of the source of the merge (which will cease to exist for all intents and purposes) will be presented just as another answer.
As Henning indicated a merge is a one-way street: a question is merged into the other. The target of the merge will keep the accepted answer, and the question statement that is kept is the version presented in the target.
I can't speak for the other moderators, but if I were faced with a flag to merge two questions, my general decision process is
- First a sanity check: are the two questions indeed exactly identical?
- If it is a case of duplicate postings by the same member, is one of them devoid of answers? In which case that one would be the source and the other is the target.
Otherwise, the choice of the source and target for the merge depends on (in order of rough importance)
- Is one question stated better than the other?
- Is one question asked before the other?
- Which way of merging did the flagger suggest?
It also may depend on things like the phases of the moon. But I never factor into consideration "which check mark to keep". Remember, check marks are not permanent, and it reflects a user's personal decision on which answer helped him the most. So I don't think it should be a factor considered for the merge process.