score the area with a box knife to cut through the paint buildup and the caulking. This way the molding will come off without pulling off the paint and rock skin.
Now, you will probably need to skim coat the areas where the skin of the rock came off. This will level out the areas so that the new paint will be smooth and level. I would use some spackling.
Then prime the areas again.
Then paint, this should get you back to norm.
If you use joint compound in lieu of spackling this is OK, but jc does shrink and you will need to apply multiple layers after sanding to build it up level to the surrounding areas.
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