There is a seal between the upped and lower units. I would replace that, plus reseal any seams and/or areas around the vents, skylights, plumbing vents, etc. An entire separate discussion can be had to cover the different ways of accomplishing that. From my experience, I resealed the seams on the roof of our Avion by first cleaning out the old stuff as best as I could, clean the surface well, then used ParrBond in the seams, covered by Eternabond Alumibond elastomeric sealant tape. I doubt I'll ever have to mess with those seams again (but I DO keep an eye on them).