Well, I can say that we're not going to stop merging threads; many of them are on the exact same issue, and it's silly to have multiple threads. In terms of reducing merges, it's something we can look into, if necessary.
Also, we generally don't merge an active conversation with one that has been inactive for awhile. However, if two conversations are active and on the same topic, we're probably going to merge them.
What constitutes "same topic" or "similar topic" is of course discretionary, and that's up to each staff member. I know the staff as a whole has given wide latitude lately in the number of new topics started, even when they largely overlapped.
It's unfortunate that replies are lost when a topic is merged; I've had this exact same thing happen to me on multiple occasions.