I had a similar issue on the bedroom slide a couple of years ago. I purchased a self-leveling caulk (clear) and resealed all the seams. The hardest one, and the one that I suspect was the issue, is the seam that is closest to the inside wall, and can only be re-caulked from inside with the slide in. It was difficult, but it worked. It fixed the leaking. I don't recall the name of the caulk, but the instructions were to smooth the bead with soapy water and my finger.
Hope this helps.
I agree that doing anything to effect the slide surface that react with the seals may not be a good idea.
Joe & Merry
'11 Ellipse QD
'10 Ford Edge Towed