Hello there! Got a phantom 3 professional "W323A", sent it for repair services due to 1.09.0060 FW upgrade, received back a "W323B". Is it normal to sent one and get back another? What are the differences between this versions?

Generally speaking, a letter designation after a model number indicates a more recent version.   (I don't know if the the American and European models have a letter designation)

As to the specific improvements between the different models, I'm only aware of these:
W323 original version
W323A New Motors / updated shell
W323B New Motors / updated shell / electronics [speculation]

I know the remote controls also received some updates (Remote controllers whose model type is GL300B can only be updated on your app)

I ordered my P3P the day they came out so I have a W323 Phantom and GL300A Controller.  When I ordered a P3A eight months later the visual difference in the motors was immediately noticeable.

If the repairs to your aircraft were too time consuming then that would have swapped it out, which it looks like they did.

Hello DJI-Ken, what I really care right now, more than why, is what. I'm sure you can, want, and will give me all the details. So please: what are the differences between the 323A and 323B aircraft units?

PJI72 Posted at 2016-9-14 11:27
Hello DJI-Ken, what I really care right now, more than why, is what. I'm sure you can, want, and wil ...

The primary differences are the new style of motors used, and to drive the new motors requires a new main motherboard.  The performance is supposedly identical to the earlier model, it is probably just easier to make the new ones.  You should not notice any difference.   Old parts are not compatible with new parts which is why they had to swap a large portion of your aircraft.  This would be a major job so it would have been easier just to swap out the whole aircraft.

Well, the answer the support gave me was: "[...] the B model is the latest revision. Model A is an earlier model. [...] The difference will be improved motors and range distance. Up to 5 km or 3.1 miles (unobstructed, free of interference) when FCC compliant. Up to 3.5 km or 2.1 miles (unobstructed, free of interference) when CE compliant "