To flush a system properly all forms of restriction must be removed, which absolutely means the expansion valve. Think of the word "Flush" think of violence. The more violent the flush the more likely you did something.
Personally I don't think there are many DIYers that can achieve a usefull flush. THe technique requires more violence than is usually used. The form of flush needs to be anticipated for different areas of the system. I wouldn't flush an evaporator unless I had a very volitile flush (one with a boiling point close to room temp would be nice - atleast the remainder could be boiled off during an extended evacuation). Trying to flush through an expansion valve would be useless if not disasterous. The little bit of flush solvent that made it through would totally stay in the evaporator without violence.
Bosch Master, ASE Master, L1
33 years MB technician