I had the same problem with much silicone used on my front end cap roof border just about over the closet area. It had been leaking issue in the past with the previous owner. Their fix was gobs and I mean gobs of silicone. All that did is just put a band-aid on the problem. As the Silicone aged it began to leak again.
I climbed up on my rubber roof and spent literally hours hand rubbing the silicone off my rig roof and end cap. I found the putty knives helped, but actually the rubbing of my palm and thumb on each and every piece of silicone did the trick. I had gotten blisters from the friction but that is how I got it all off. Eternabond will not stick to silicone...read the instructions and website and you will see that warning.
After that I put 4" Eternabond over the seam between the cap and rubber roof. 8 feet across the rig from side to side and turned it down the side wall to the edge of the rain gutter. It covered the seal perfectly and I have had no leaks since.
Once the eternabond was on and properly rolled and seal pressed, I scoured the entire roof with warm soap water and a scrub brush let the roof dry in the sun and when dry, put a RV rubber roof seal on the whole rig.
I used Heng's Roof Coat Rubber Roof Coating:
Rubber Roof Coating for RV / Camper / Trailer (Quart) on eBay!
see attached picture of the RV roof completed.