I have heard there are replacement seals of varying quality, and a bad one will leak more than the one it replaced. I would check on the source of your new seal before insisting it be installed.

You can also run a bead of black marine grade sealant around the whole perimeter, glass side and metal side, but leave a section of rubber-to-metal unsealed along the bottom to allow for drainage.

If your aluminum trim around the window is still in good shape after the job, I would say he knows his stuff. But I would still question his decision, since its the same amount of work to reuse the old seal.

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1985 380SE Blue/Blue - 230,000 miles
2012 Subaru Forester 5-speed
2005 Toyota Sienna
2004 Chrysler Sebring convertible
1999 Toyota Tacoma