I know your frustration. I had the same problem last week. I never did find the exact cause. I had updated a part file and then made a bunch of changes to the assembly (part locations, spacing's, and mates). I had turned off Flow so I wouldn't get a ton of error messages for every new mate and adjustment. When I turned flow on and went to correct material properties I ran into the same problems.
My only solution was to dump the assembly and part file and start over with backup files. Avoiding the change to the part file and leaving Flow turned on I was able to make all of the adjustments. I did one or two at a time and then performed a Rebuild. If I ran into a rebuild error I would dump the file and reload the last good file. I eventually able to make all of the changes but never did find the root cause.
Being faily new I have run into several unexplained problems similar to this. I have atleast one at tech support that still has not been figured out. I think Flow is a little more touchy than most programs. Maybe it is just a sequence thing. Hopefully it will get solved.
I've seen this in the past (not sure what I did to cause it)
the solution was always to edit each material definition - make sure it still includes all of your intended bodies. Sometimes everything was still correct and you just hit ok. In a given material definition SW somehow lost track of one of the solid bodies - sometimes all you have to do is edit a body and it changes the name of the body (i.e. from Extrude <13> to Extrude <14> because you added another extruded feature).
Or if you delete a body it still has it in the list of bodies that a material should be applied to so it complains that it is trying to apply a material to a body that no longer exists. (this is when simply editing and clicking ok solves it)