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Would you trust the typical lizard or snake to prepare your taxes?
When the spell feeblemind causes the "[t]arget creature's Intelligence and Charisma scores each drop to 1 [and makes it so that t]he affected creature is unable to use Intelligence- or Charisma-based skills," that's the last the spell has to say about its effect on the creature's skills. While ability score damage and ability score penalties don't cause a loss of skill points, ability drain "might cause you to lose skill points [sic]," but the effects of feeblemind? Not a word.
This GM thinks it's okay if the creature affected by the spell feeblemind keeps its skill ranks intact. The spell's effect already prohibits the creature from using skills with Intelligence and Charisma as their key abilities, so the creature's limited to Acrobatics, Climb, Disable Device, Escape Artist, Fly, Heal, Perception, Profession, Ride, Sleight of Hand, Stealth, Survival, and Swim. That's a tight enough list that's restricted further by the spell's effect that causes the creature to be unable to "understand language… or communicate coherently." That means, for example, no matter how many ranks the creature has in the skill Disable Device, it's liable to lick rather than disarm a symbol of death, and no matter how many ranks the creature has in Profession (accountant), the creature's days as an accountant are (ahem) numbered.
While allowing the creature to keep its skill ranks likely sacrifices verisimilitude on the altar of playability, the creature affected by the spell feeblemind is already essentially a useless, idiotic wallflower. This GM sees no need to rub it in by also taking away the creature's skill ranks.
Note: If it matters—and it really shouldn't—the GM would have a creature affected by the spell feeblemind recompute its Intelligence-based and Charisma-based skill modifiers for its new Intelligence 1 and Charisma 1, therefore a −5 penalty instead of its previous ability score bonus or penalty.