In the first sentence, the words run and over must be considered separately:
run (Cambridge Dictionary) to (cause something to) travel, move, or continue in a particular way
over (Cambridge Dictionary) across from one side to the other, especially by going up and then down
It seems that the speaker is talking about a necklace that has some sentimental value. The necklace has a butterfly pattern on it. Occasionally the speaker takes out the necklace and moves his fingers across the surface of the butterfly part of it.
In the second sentence, run over is a phrasal verb that has a very specific meaning: (Oxford Dictionary) Go over (something) quickly as a reminder or rehearsal.
This simply means that the she is thinking about the plan, but in a superficial way.