Silicone remover works fine, use it. I wonder with the eternabond if you prepared or cleaned the area properly? It should stick. Waiting for warmer weather or getting to a warmer spot is going to make for better repairs.
My inclination would be to stick with eternabond, first removing alll the caulking from the seal, reseal with a Dicor roof caulking product, then apply eternabond over that after preparing the surface as directed.
I do all my own stunts
03 Dolphin LX 6355, Workhorse W22, 8.1 vortec, 04 CR-V, Blue Ox, Brake Pro----Norm, Barb and
Doc(He's a PhD)