I had the plate disappear also but didn’t get a check engine light. Whipple was nice enough to send me a new tube free of charge.
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Black high temperature silicone, that’s fuel resistant also. you just have to wait till it dries or you put self tapping screws in that have flat heads , no way their pulling in, plus they seal. I went the silicone route.What did you do to fix the holes? I just taped it up but looking for a better solution.