I tried that with my messenger bag and the heat released the lining as much as it remelted. The heat tended to warp the fabric. I had better success removing the lose lining and retreating with a waterproofing spray.

I read about heating the liner to get it to re-adhere to the fabric. I was not successful with this approach did not get consistent results. I finally scraped off the remaining loose liner then applied multiple coats of spray on waterproofing. This is not ideal, but the bag continues to be useable without shedding TPU.