Server merging seems very complicated, I'd like to propose a much simpler solution:
Server Gates: Individuals in a server could invest wood and other resources into creating and opening Gates to nearby servers - the farther the server is away in server number, the more expensive it would be to open the gate. A design for a gate could be bought from the new Alchemist for 100,000 gold. A few million wood (or some very large number that requires cooperation) would build a frame and then it would take a concerted expenditure in elixir to keep the Gate open. Multiple gates could be started to different servers, but only with the cooperation of a LOT of people on a server, could they actually be opened. You could even have a warning in servers that are being built toward that an enemy server (with a progress bar) is trying to attack - this might change the strategic calculations if people know another server is invading soon...
Once a Gate is opened, players could travel between them freely - raiding and plundering on either side. Maybe you could allow migration between kingdoms connected by Gates. This keeps the "story" integrity of each server - we've consolidated our server into a single color because we wanted to work together before a server merge.
This solves so many problems: You don't have to figure out all the messiness with Houses, towns, ownership and duplicate accounts on merged servers. It gives people something to work toward collectively and be strategic about who they want to fight - let us do the hard work of finding good targets and opponents. Also, just in one quick fix, it doubles all the PVE opportunities - players would now have two (or more!) servers to attack dungeons and rob caravans.
I know you've already put some thought into server merges, but I hope this is still useful to the Devs. Keep up the good work - looking forward to the update with crafting and the Rakan.