I have seen the "water barriers" behind many many a door panel that I have removed. I have removed and did what is needed and then reinstalled them. Typically there is a pliable sealant that holds them in place while you reinstall the panel.I'm no expert on the inside waterproofing criteria of doors on these trucks, but I've removed the plastic inner shell of the door on many other vehicles for a myriad of reasons, and I've always found a large heavy plastic sheathing covering almost the entire door panel and sealed on top and sides to the door's metal frame, in order to keep water our of the inner workings and components of the door.
@OR VietVet Are these truck door water seals different that most other vehicles on the market - i.e. no plastic sheathing for waterproofing in the door?
The outer wipe seal is the first layer of defense against the water/rain. The second is the wrap around seal that the window moves up and down in when it lowers and rolls up. The other is the door opening large/long rubber seal that the door closes against.