Yes; we have had loads of complaints down the years (though, interestingly, I haven't seen one recently) of people doing exactly that, mucking about with both Flying Blue and Skymiles numbers (invariably the combination that leads to complaints here; but don't take that as meaning that it is only an issue when mucking about with those 2 FFPs, it's just that they are the 2 most frequently-encountered Skyteam programmes on Flyertalk so it's the most common "crossover" that people using FT may have) that, although they "successfully" changed the FFP number, and although they finally flew with a boarding pass showing the "correct" FFP number, the miles still went to the "wrong" account.

I would advise you not to rely on this strategy except as a once-off or a stop-gap; you should consider how the change of alliance on September 1st affects things for you personally, and come up with a strategy - involving favouring one or the other programme - that works best for you.

Despite the constant chatter on these boards about the "rumour" of EB being folded into Flying Blue, I do not see that that is likely to happen; even if it does, it's not going to be immediate and you will still have a period where both programs exist separately, within the same alliance, so be prepared for that scenario.