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Nah, that's the beauty of the "clean slate" that's created after 30 days of elimination. You aren't automatically going to have a negative reaction just because you've avoided something for 30 days. It carageenan makes you itchy, or soy makes your fingernails hurt, that's going to be a specific thing you're going to want to take note of. We can all "get used to" stuff and have a "new normal" --- that's why people who move from Oregon to Nevada all of a sudden report stuff like "holy crap, I can breathe better!" If they just lived in Nevada for 30 days, then moved back to Oregon, well, sure, after 30 days in Oregon they probably wouldn't be conscious of the fact that their sinuses are all clogged up from mildew and whatever, but that doesn't mean Oregon is a friend to them.
I did some digging on this REALLY OLD topic today (those of you getting a ping, please don't hate). I'm jumping to a conclusion here, but I think that Chipotle has stopped using Soybean Oil in the way that previous posts have described in this thread. In posts dating back to 2012 and 2013 other members have mentioned that Soybean Oil was used to cook all meats except the carnitas. Today (Jan 7, 2016), Chipotle's ingredient list website shows that all meats are cooked with Rice Bran Oil, and NOTHING is listed as using or being cooked in Soybean Oil - not even things other than meats - "Soybean Oil" and "Soy Oil" don't even appear on the entire page! The only mention of soy at all is in the Sofritas, a soy-based meat-substitute (it's kind of required that it contains soy!).
SO! My conclusion-jumping was to assume that they have replaced Soybean Oil with Rice Bran Oil. And since Soy is a known allergen to many, it would make sense for them to make this move, as they are a conscientious business.
The Chipotle website does still make some blanket statements about cross-contamination always being possible, and that there are no guarantees that a particular ingredient doesn't end up where it's not supposed to. (Hello life, where there are approximately zero-point-zero guarantees!) If you are an ultra-pure-purist, then you might decide that Chipotle is 100% out for you because the Rice Bran Oil or Soy from other foods, could just maybe end up in your meal. The blanket statement also points out that this could happen in the field, or in processing the food before it gets to Chipotle. So, the old adage: YMM.
Looking back at the ingredients list and allergen statements, we see that the Carnitas is cooked with Sunflower Oil only, and all other meats are cooked with Rice Bran Oil. Rice Bran Oil is NOT Whole30 compliant. Sunflower Oil is something Whole30ers should avoid when possible, but is almost unavoidable in the dining-out world. So all meats, except for Carnitas, are still ruled out. Boo. But Carnitas are daggum yummy in my book, so I'll take it as a win - after all this still means (to this guy) that Chipotle CAN BE Whole30-compliant, when done right.
But what else can we have? Fortunately that list is shorter than what we can't have. Well, I say "fortunately" because that means it keeps things simple, and I'm a fan of simplicity.
Based on the ingredient lists and allergen statements, I believe the following to be Whole30-compliant. BUT I AM NOT A WHOLE30 EXPERT </legalDisclaimer>.
Tomatillo-Red Chili Salsa
Tomatillo-Green Chili Salsa
It is worth pointing out, specifically, sadly, that the Fajita Vegetables are NOT Whole30 compliant because they are cooked in Rice Bran Oil.
But, as a previous poster pointed out, we can try asking for RAW veggies! WHOOHOO! Maybe if enough of us ask Chipotle's Corporate Machine to try using the Sunflower Oil on the veggies, instead, perhaps they will. Perhaps they will.
dang, wish you would've made this post yesterday instead of today : I also baked bone-in skin-on thighs yesterday, but just seasoned them with salt & pepper. Tasty but boring; now I know what to do next time!