Boat Life makes a liquid sealant, never used it but see it on the shelf, may be easier to get in there and drip it in, than push in caulk. Try to clean the gap a bit when you pull back the rubber - with denatured alcohol to get a good bond.
If it is cool out, use a hair dryer to soften up the rubber - makes it more pliable - don't rip it.
I use other Boat Life products, Life Seal and Life Caulk.