Now that's a new one on me Scott; I've never heard of a manufacturer installing windows wider than the sidewalls. Are they implying the window is actually thicker that the width of the sidewall? I'm not ruling that possibility out, but it seems unlikely, if not impossible to do. Here's a diagram of how most RV windows are installed.
Removing, sealing and reinstalling the windows will not make them any less deep. You can verify if indeed the windows need resealing by simply using a garden hose and see if any of them leak. If any water intrusion is evident, then he is correct; they need resealing. Water intrusion is one of the key maintenance areas that requires sincere diligence, so it's not to be taken lightly. Still, an adequately equipped RV handyperson should be able to remove, reseal and reinstall the windows. Be sure to remove all remnants of the old sealant. Most RV windows simply "sandwich" the sidewall between the outside window and an interior metal garnish trip piece. It will take two people, but it is doable.
Here's a related question and how to remove RV windows for resealing.