i don't see why not... Though if you want to take an extra precaution, stop the BE services first.
Note a B2D and a dedupe folder are not the same thing. A B2D needs to be defragged if you are not allocating all the space up front. a dedupe folder writes its files fully allocated up front, even if you only backed up 1MB, it'll write the 256MB files regardless. So that there is less chance of fragmentation. The container file will "fill," with other data over time.
