My lower seal was flapping in the wind also, as the rubber wouldn't stay into the plastic. I simply cleaned the rubber, and windshield, and used some 3M double faced tape to make that tight seal again. Seems to be working good so far.

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95 SL500 Smoke Silver, Parchment 64K
07 E350 4matic Station Wagon White 34K
02 E320 4Matic Silver/grey 80K
05 F150 Silver 44K