Encased Fans are basing their wind direction on the rotation of the shaft, as viewed when looking in the positive direction along the coordinate axis, instead of as viewed in the direction of the fan.

This means that if I have two Fans facing in opposite directions, and both receiving a clockwise rotation (when looking at the back of the Fan), the fan that is facing towards positive (X/Y/Z) will be blowing air, while the one facing towards negative (X/Y/Z) will be sucking air.

As a result, if I take a contraption, and rotate it block-for-block (or build the slightly contrived contraption below), there is a reasonable chance that any fans will switch direction.

Sadly, fixing this now will break a lot of setups. May be a candidate for 1.15

Unfortunately, it feels like you're closing the door after the birds have flown the coop…
Now that you can move fans, it's not hard to imagine someone wanting to create something like this:

As an alternative, could I suggest adding the ability to reverse the direction of fans with a wrench?
Theoretically (and apologies if this isn't actually reasonable, or doesn't fit with your vision for Create) you could make it so that fans that are in-world when the change happens are automatically reversed if they're facing the negative direction on their axis…