The a/c is one place I don't like to take shortcuts or do anything less than a perfect job. How much trouble would it be for you to flush the evaporator? For example, I have compressed air at home, so for me it's no big deal.
The service advisor may be right, but wouldn't you want to make sure before you put everything back together, and went to the trouble of evacuating and recharging the system?
BTW, are you doing a conversion at the same time? If so, you should probably flush regardless of the filings.
95 E320 Cabriolet, 131K