The plumber is correct in that the treated water would be cleaning out the pipes that are in the house and with the deposits that are with in the pipes.
Galvanized Steel? There might be some as in nipples but the whole house? metal detector time...
Now the question would be how much of the plumbing is still of the older style.
You say that the house had some work done in the 90's and then around 03' was any of that the plumbing?
If the pipes are with in walls that are not open then there could be a challenge.