Well, patch notes were very specific that stats don't carry over if your status switches from one leaderboard to another (but your old stats are remembered if you ever switch back).
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In the above example, if the player had been pledging Loyalty to that Faction for the first time, their Leaderboard stats as a Loyalist Pilot for that Faction will start at 0. However, the stats they accrued while operating as a Mercenary Pilot will be remembered by the system; in the event that the player returns to the life of a Mercenary, their stats will continue from where they previously left off.
If that player instead later pledged Loyalty to a different Faction, again for the first, their stats would again start at 0 as they have not accrued any stats while sworn to that Faction.
Furthermore, nobody who picked mercenary or loyalist has had the possibility to get out of that contract yet.