Ok, I would recommend removing the trim and the corner moldings, clean, reseal, and reinstall. You can buy tubes of Butyl at the box stores. The thing about gunnable butyl is that it is better than factory install, but you have to place it correctly the first time. If you you have to pull the trim back off you will have a mess until it sets up.
Your pictures show that there is possible damage to the decking. If you can pull rubber up for a week or so inside of a building so that it can dry, cause I am assuming it is wet, then add more screws to the trim and seal over the top of them. The butyl is going to be key to use as a primary seal. Alpha self-leveling is a secondary sealant.