Caulk Crack

So I've been working on my 1968 4 door, and I keep looking at these cracks thinking, man it cant be all that good for water to sit down in there. (I've blown out with air compressor after washing)
I'm wondering if I should just smudge some new stuff on or what an easy way would be to get rid of this problem, thanks.
Also going to attempt to adjust my back doors to not hit.

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I would scrape it out. Clean the rust , Epoxy prime and re-caulk. Rust never stops and there is rust under there for sure.