
Zephyr Runeglyph |

1) Yes. It would be kind of silly for Paizo to give the Eidolon class skills if it didn't get class bonuses for those skills.
2) No. Those free evolutions are part of its base form, and the base form is permanent upon selection (unless you use the Evolutionist archetype but even then, it wouldn't work they way you're thinking). It's worth noting you can replace certain free evolutions when explicitly noted (like the Biped's claws with slam), but this costs points to do.

Maezer |
Eidolon class skills are:
Bluff (Cha), Craft (Int), Knowledge (planes) (Int), Perception (Wis), Sense Motive (Wis), and Stealth (Dex). In addition, at 1st level, the summoner can choose 4 additional skills to be class skills for his eidolon. Note that eidolons with a f ly speed receive Fly (Dex) as a free class skill, even if they do not gain a fly speed until a later level.
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Nothing in the rules lets you exchange the free evolution. Besides there are no other free evolution to exchange them for so even if you could refund them back, adding 0 points to your evolution pool doesn't net you anything.