Scupper Repair Leak

Have a flat roof. Surface area is rather small given it’s a porch roof. The roof was done about 5 years ago. Recently the plaster ceiling cracked and partially collapsed. The roofing company determined it was due to an improperly sealed scupper and fixed it thankfully. When their rep came he said the rain gutters should have been removed when the roof was done. I’m not sure why but he seemed to imply that was part of the cause for the leak. I am a novice at this but my understanding is the components are a scupper, conductor head and a down spout. Why would the conductor head or down spout require removal? If they didn’t remove it to perform the repair, is this a problem? I was told they used mastic and silicone to make sure the scupper wont leak again. What to think?