Yeah, I would say paint is a bad idea and won't work. And to make it more annoying, you will have to grind/sand it back off in order to prep for glassing.
It's remotely possible you could get caulk to work somehow, but I don't think it really would ('course I'm not looking at it - any photos?) and it would be yet another mess to clean off to do the repair right.
Again, I can't see your issue, but just to take an example that is somewhat easy to describe. Let's take the example of a cardboard box again. Say the side and the bottom are made from two separate pieces of cardboard, and then 4" masking tape holds them together. The cardboard is your bulkhead, and the tape is your tabbing.
If that tape failed, I would cut out any loose tape with a utility knife (and or Multimaster or other tool), then sand/grind (i.e. coarse paper, something like 60 grit) until I have smooth surface with nothing loose. If there is gelcoat and it is tight to the surface, you don't need to get every last trace off. Then I would mask everything off (to keep it neat), clean the area to receive the work with a solvent, and then, if there is a 90º corner (such as at the box bottom), I would thicken some epoxy and make a fillet (which is sort of like a little bead of caulk that turns the 90º corner into a mini-45º corner). Over the fillet I would put new tape (you can buy this as tape - neater than cutting strips from a big sheet), soaked in epoxy resin. Roll it all down (or squeegee) to make sure the air is out, and let it cure. Then you can paint over if you like (necessary if it will be exposed to UV).
I'm sorry if this sounds like too much of a pain, but if your issue is what I'm visualizing, then it's probably the way to fix it "right." I can recommend a really good free "book" that you can get online that describes and shows all this with clear line drawings. It's put out by WEST System epoxy. WEST is a great brand, and often easiest to find locally, but the same will apply to any good epoxy (i.e. not hardware store 5-minute stuff).
If you go to this link, then each of the illustrations you see will be a chapter of the book (which is also available in paper form).
http://westsystem.com/ss/use-guides/
I re-did parts of my rubrail last summer. They are put on with rivets. I went back with screws. There is more detail here (and also in some other threads if you search - I got inspiration from those who had gone before me).
Rubrail starts about 1/3 of the way down this page:
http://www.c-brats.com/viewtopic.php?p=267126