I don't think it is necessary to remove the old caulk. The area where the Eternabond is going to be applied needs to be very clean. I clean the roofing membrane itself with alcohol; it will remove the surface dirt and chalking. After an initial cleaning with the alcohol, do it again - then use a rag or paper towel and rub the membrane surface again to remove residual chalking. For the caulking itself, I use a rag dampened with naphtha - which will damage the membrane and the glue that holds it down, so don't allow the naphtha to get onto the membrane; mineral spirits would work well, too, but it does not evaporate as quickly as naphtha. When applying the Eternabond, don't expect it to be perfect when going over an uneven surface - it does not like to stretch over irregularities. Use a roller to roll firmly over the Eternabond to get it to stick well. Expect the Eternabond to stick the first time it touches anything - it is very hard to re-position it if the initial "stick" is in the wrong place.
