Shane is stop on, as usual.
Any files that are open are usually "locked". And when measuring, duplicating and balancing, StableBit DrivePool avoids locked files, since we can't ensure the state of these files while they are locked. (which is part of why they get locked by the OS, in the first place, so nothing else can mess with them).
Once they're no longer locked, they should be fine, and should be updated during use. Though resizing VHD files are ...tricky. And if you have the space, fixed sized VHDs would be better to use, if they're stored on the pool.