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It's impossible to value Chipotle shares right now

Where’s the bottom for Chipotle?

In order to determine the value of a stock, or for that matter any company, the predominant approach is simple: Estimate how much that company is expected to make, and then multiply that expected earnings number by an "earnings multiple" that takes into account the company's expected future growth.

The bad news for those who wish to assess the value of Chipotle is that each of those numbers is a complete mystery.

When Chipotle updated shareholders about the impact of its E. coli incident on Dec. 4, it predicted that same-store sales would drop 8 to 11 percent in the fourth quarter, and rescinded comparable restaurant sales guidance for 2016 (after predicting a single-digit increase in October). Chipotle also announced that it expected to see $6 million to $8 million in the fourth quarter to deal with food safety issues, but made clear that this "does not include any estimate for legal claims and related expenses."

This guidance from the company came before a Chipotle in Boston closed for nearly three weeks after 136 patrons contracted norovirus, an outbreak that was said to be unrelated to the E. coli cases. It also came before the CDC reported that people who ate in two Chipotle restaurants in Kansas and Oklahoma contracted a different type of E. coli, bringing the total number of states involved to nine.

Read MoreBoston Chipotle where 136 sickened with norovirus reopens

With the potential sales and legal impacts up in the air, analysts are naturally having a dog of a time adjusting their earnings estimates for 2016.

In a note released shortly after Chipotle's new guidance, Piper Jaffray analyst Nicole Miller Regan noted that the company has experienced "severe volatility in same-store sales trends" in the fourth quarter. Regan goes on to forecast that the company will earn a total of $13 per share in 2016, which is in line with the earning reported in the first three quarters of 2015 alone. She does not provide a same-store sales forecast.

Matthew DiFrisco of Guggenheim, meanwhile, expects Chipotle to report a 4.8 percent drop in same-store sales in 2017, which translates into $13.80 in earnings per share, slightly above Regan's number.

Far more optimistic is BTIG's Peter Saleh, who expects a far-less-steep decline in same-store sales in early 2016, and consequently sees a much milder impact on earnings. Actually, he continues to forecast considerable earnings growth in 2017.

Read MoreAnother bad number for Chipotle

The bitter truth is that no analyst can know how much this company will earn. While this is probably always true, it is particularly true in Chipotle's case, when so much about the multi-region E. coli outbreak — particularly the key question "Which ingredient caused it?" — remains unknown. As DiFrisco observes: "Meaningful improvement from current negative [double-digit] SSS trends will likely require: 1) a CDC conclusion on what the root cause was, and/or 2) ample time from any linked cases and public trust is restored."

"The estimates are all over the board all over the street," Saleh granted in a phone interview with CNBC. "And everybody could be totally wrong. We're trying to estimate off of negative-double-digit comps in November, and it's really hard to do."

When asked how he made his specific call on same-store sales in such an environment, Saleh responded: "We have to make a forecast. We can't just discontinue our same-store sales estimates. So it's as good an estimate as you could come to."

To come up with an accurate earnings estimate, analysts actually need to go even further, predicting what the end result of legal action will be and how Chipotle will change its processes, in addition to how consumers will respond. Given this fog, forecasting earnings probably becomes a special type of fool's errand.

Read More Chipotle metric drops to lowest level ever

Perhaps even harder is predicting the behavior of investors.

Chipotle is famously a growth stock, trading at an average of 52 times reported earnings and 39 times expected earnings over the past two years prior to October, which is nearly double the valuation multiples accorded to its hotel, restaurant and leisure peers in the S&P 500, per FactSet. Actually, even given the health scandal, Chipotle shares are still commanding a premium valuation (30 times next year's or last year's earnings, versus a respective 22 and 25 for the group).

So how will the scandal affect Chipotle's earnings multiple, which has clearly been reflective of enthusiastic expectations?

Unsurprisingly, the analysts are divided.

"Amid negative double-digit SSS, we assume shares will trade at a discount to its historical mean P/E," writes Guggenheim's DiFrisco. He assigns a multiple of 25 to 30 to his 2017 earnings estimate, which yields a pretty wide target range of $475 to $570 (though with a neutral rating, he has not official target on the stock).

Saleh, on the other hand, is keeping his foot on the gas. "We believe Chipotle can recover from this issue and the outbreak will not impact the company's long-term growth or sales trajectory," he wrote, which lines up with the 37 times earnings multiple he slaps on his high earnings estimate.

Never mind that the scope or root cause of the "issue" remains unclear, with the Center for Disease Control's investigation ongoing. Never mind, as well, that the company's multiple will not be based solely on the company's sales trajectory, but on investor expectations about the sales trajectory as well.

"Valuation is not necessarily a straight science. There's a little bit of art involved, as well," Saleh said. "Now all of the sudden the world hates Chipotle, but who knows what the next two months will hold?"

For investors, all of the question marks around the stock should probably serve as a red flag to stay far away.

"Drawing a line in the sand and saying, 'The bleeding is over' is an impossible case to make," said David Seaburg, Cowen head of equity sales trading, in a Monday "Trading Nation" interview. While it may present a long-term value, "near-term, people should just stay the heck away from this thing."