Yes it will. For one thing, the money script will not run for the remainder of the turn. Same holds for population replenishment scripts. The more factions that need to have their turn, the worse its effect.
Eleutheroi turns are relatively safe on these counts.
In my experience though, it often leads to various script "novelties". According to one character it might be spring, according to another Winter / Summer movement restrictions may apply. This also seems to be true of Autosaves.
In general, the best course of action is to save your game before you hit the end turn button. If you are forced into battle, reloading that save game at another point in time (if you have to leave for work / school / whatever) should result in the same AI behavior.
Bookmarks