If you're playing factionA and use "control factionB" the remainder of factionA's turn will be turned over to the AI. When factionB's turn starts you'll have control of factionB. Again, as soon as you use "control factionA", the AI will complete factionB's turn. So if you move the army out of its settlement, there is a good chance that it will move right back in unless you expend all of its movement. Whether or not this actually happens, I can't say.
Doing this in EB will probably screw up some special events executed by script and may upset some of the financial assistance given to the AI.
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