The Project Consultant came out yesterday and he agreed the membrane needs to be re-installed with a water-based glue. I will also check to make sure there is a board over the decking. I’ll post a photo here after the new membrane is installed.
The epdm needs to be replaced and installed properly. For that small of an area there is no reson to reinstall the same rubber, who knows what the original installers did to it under the shingles.
The project consultant agreed a new rubber membrane needed to be installed. He was the lead on re-doing the project and he spent a few hours with the foreman adhering the new membrane. The piece seems to go up further now under the shingles, and he added a metal piece at the end to help extend the run-off onto the lower roof. Thanks for the help and advice!