After a similar incident, I had my wheel wells coated with Line-X spray-on truck bedliner. I feel like it adds some protection to the inner fender. Time will tell I guess. I also purchased a TPMS and replaced my tires with Maxxis tires for piece of mind. I wasn't so lucky and had to change my tire on the edge of a busy freeway.
Sorry, I can't recommend anything for the black fabric that was damaged under your trailer. I know it is a vapor barrier and blocks moisture in one direction while allowing air to breath. You might be able to tape in a patch using vapor barrier tape (the red tape you use on house wrap), but I'm just guessing.
Thanks for sharing.