Here's the description from the VAG workshop system (interestingly it says NOT to remove the carrier):
Problem description
Doors, water getting into vehicle interior through the joint between the door assembly carrier (bottom) and the inner door frame.
Cause
Rubber seal around door assembly carrier not watertight.
Production solution
Change in watertight seal fitted to the door assembly carrier or plate.
From 12.01, Chassis No. 2R 067365
Service solution
In all cases where water is entering the vehicle interior around the door, carry out the following checks before replacing any parts or attempting any kind of repair:
1 - Check to see if the water is coming out through the bottom of the inner door trim panel. If the water is coming from this area, remove the trim panel.
2 - With the trim panel removed, check to see where the water enters: through the wiring harness clip, the rubber grommet, the window glass fixing screw rubber cap, the door trim clips or screws OR through the rubber seal around the (bottom of) the door assembly carrier.
3 - If the water is entering the interior via the watertight seal on the carrier, and the chassis number is earlier than the one given above, (under the heading of Production), proceed with repairs as follows:
The rubber seal on the carrier plate should be repaired without removing or loosening the carrier plate bolts. Apply bodywork paper to the area around the joint between the inner frame and the carrier plate.
Apply the two products which make up adhesive kit KR00430003 to the area around the joint where the paper has been applied: first the paint primer and then a bead of between 4 and 7 mm of the sealant.
Once the sealant is completely dry, check again to see if water comes through before refitting the door trim panel. Also check whether the holes on the inner lip or edge of the rubber trim around the bottom of the door are blocked. If they are blocked, make the necessary holes on the inner lip of the rubber trim.
Never make any holes or cuts on the outer lip of the rubber trim around the bottom of the door. This will not solve the
problem of water entering the vehicle and will actually create a new
problem with dust getting into the vehicle.
4 - Check too whether the drain holes in the doors are blocked with wax. The holes are easily visible if you lift the rubber trim.
If the holes are blocked with wax, remove the lower door trim and apply gentle heat to the area to melt the wax which will then drip out through the drain holes and leave them clear. Refit the door trim.