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The picture clears some things up. You say seam, and I have to guess that the patch is attached only at the perimeter. I'd still suggest any good seam sealer on the inside, and perhaps even taping...

First, what sax is that?

Second, cotton don't seam seal very well. Try tar.

Edit: Actually, as others suggested, I'd try silnet first. How big is the embroidered patch? You might consider...