If the right one is not hitting then it is likely that only the left is bent.
When the trunk is fully open, compare the gap between the right hinge and the edge of the trunk opening on the body with that of the left hinge and the forward edge of the trunk opening (the transverse body section between the trunk lid and soft top lid). The gaps will be different. The difference is likely due to the left hinge being "sprung" a bit as a result of some past pressure on the left side of the trunk, either as a result of wind or other force when open or a past shunt to the left rear corner of the car.
Before you remove everything from the car, try detaching the trunk lid only from its hinges. Outline the position of each hinge on the trunk lid before removal. With the hinges "down" compare how they lay in relationship to each other and the edges of the side opening along the rear fenders. Measure the distance from the forward edge of the trunk opening (the transverse section between the trunk lid and soft top lid) to the where the "curve" ends and the flat area to which the trunk lid attaches begins.
In a perfect world the flat areas should be parallel to the side edge and equidistant from the forward edge. The left hinge will probably be higher than the right hinge and the distance shorter as well.
Then compare the angles of the hinges when they are fully "up" as far as they can go. They should be parallel to each other but won't be. You will likely find that the left one sticks "up" and is perhaps more "forward" more than the right one.
The task is to correct the angle of the left hinge such that it parallels the fully closed position and distance from the forward trunk opening of the right hinge, and the curvature and fully open angle of the right hinge. When done they should mirror each other in both the fully open and closed positions.
As to how to actually reshape the hinge itself, you may be able to build up a stack of wood planks in the trunk to a suitable height to be able to bend the hinge down and rearward against the stacked wood in stages until its shape mirrors the right hinge. The specific area that needs reshaping is that area of the "curve" where the paint flaked off. Using planks should spread the pressure exerted on the trunk floor over a wide enough area to prevent damage to the floor, and soft wood like pine under the hinge itself ought to be soft enough to absorb and minimize some of the bending stress on the hinge itself.
Since the object of the exercise is to reshape the left hinge to mirror the shape and position of the right and no tweaking was done to the right hinge, on reassembly you should be able to secure the trunk lid to the right hinge to exactly as it had been before disassembly. The final positioning of the left hinge to the trunk lid will be a matter of loose fit trial and error until you get just the right fit of the trunk lid to the opening when closed.
