Erk, that's not supposed to happen! Just to clarify, you said it was on iOS but also that you connected with Facebook, but the Facebook login is only on desktop. Do you mean this happened on desktop?
On iOS even if the local profile is wiped (if you deleted the game, for instance), as long as you've been signed in to Game Center the game will pull down your achievements which will unlock the cities. The profile is also synced to iCloud by default. If you restart the app again, has it still not unlocked the previous cities?
On desktop if you're signed in to a service that stores achievements (Steam or GOG) then it'll also pull down those achievements if the profile is wiped. Steam also syncs the profile to Steam Cloud.