This is mainly for the lyran/davion merger and de-merger historical events. If you have a retainer contract with either of them, it doesn't transfer to federated commonwealth when they merge, and if you have a retainer contract with the fedcom, it won't transfer to either Lyran or Davion when they split.
Historically speaking, all the merc units on retainer contracts with either just carried on after the merger/split so mekHQ should probably do it that way too.