Honestly, an idea I'd throw in which will probably never happen, is that you merge servers at seperate times. (Did I word that right?)
Example: Let's say Server A and Server B merge. Anyone from B who joins a clan from A is safe. Then after a little while, anyone that wasn't in a Server A clan who is from Server B will get seperated back into Server B. Then A merges with a third one, Server C. Then rinse and repeat. It'd be a nice way for people to meet other people rather than stay with the same old faces as LegendaryUchiha said.