First, I would try to confirm that the seal is really the problem. Mine had a leak, but it was above the bed hatch as well. Get a moisture meter and see if you have wet readings for the walls above the hatch; if yes look higher. The rear marker lights each have a hole behind and can be a leak point, as can the seam between the roof membrane and the wall. I used Eternabond over the seam and sealed the tops of the marker lights.
Next, is your bunk sealing properly. If you have the cargo bar type of system (there are at least 3 different closing mechanisms on the hybrid line over the years), make sure sure that it is still applying sufficient pressure to the door to seal. There are rubber pads on each bar, and if they are dried or have fallen off, the door may not be getting a tight seal. Replace missing pads, and dress old pads to restore.
Next, check the bunk seals. If they are dried or cracked either rejuvenate or replace. There are rubber protection products at your auto-parts store that will restore a lot of the give in the rubber. Replacement seals can also be purchased.
If you still have trouble getting a seal, add a thicker seal, or an extra layer. The previous owner of my HTT added a bit of foam weather-stripping to the trailer side of the sealing surface to add a little more protection.
Finally, take a look for several other posts here in the HTT section for those of us who have repaired our floors. There are a couple hear and in other forums as well. Just be aware that fixing a floor on a laminated construction trailer might be a bit more challenging than a classic trailer construction as there are probably two different layers of rotted wood on either side of the sandwich.
Good luck to you!
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2011 Jayco X19H (purchased 2015)
2008 Jayco 1007 PUP (purchased new, traded for the X19)
2018 Nissan Titan Midnight Ed.
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