"They look at the stock price and they feel that the future of Apple is bleak," he said. "They feel their talent could be more useful elsewhere than at Apple."
While Chowdhry still has a $650 price target and overweight rating on Apple's stock, he said his firm may revise its outlook after the company reports earnings.
"We are waiting to see what Apple says in earnings. If they are disastrous and they don't talk about what they are doing to keep employees and continue to talk about share buybacks, then I don't think it's going to work out for Apple," he said.
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Gene Munster, managing director and senior research analyst at Piper Jaffray, said Apple's stock performance, which has fallen about 25 percent this year, and employee morale are closely linked. He said coming product launches may help restore the morale and the stock price.
Munster, who has a $655 price target with an overweight rating, said there's a 95 percent chance Apple will launch a cheaper iPhone this year. He said he also expects the company to unveil a television set and possibly an iWatch sometime next year.
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"The morale is partially tied to the stock. That 's why I think it keeps coming back to these products. And the reality is that if these products are what we expect them to be, that should get the stock going and that should be good for morale," he said on CNBC's "Power Lunch."
"Big picture, it's been pretty lethargic on the products over the last six quarters and we should see a measurable uptick which ultimately should give us positive earnings revisions which I think the stock desperately needs."
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But investors shouldn't hold their breath, growth is still looking pretty sluggish for the company in the near term, analysts said.
Misek, who cut his price target to $405 from $420 on Monday, also slashed his estimate for iPhone orders for the rest of the year.
The company is expected to make 25 million to 30 million iPhone units between July and September, Misek said in a note to clients. He had previously estimated 40 million to 45 million. He also made downward revisions for the holiday quarter, estimating that Apple would plan to make 50 million to 55 million iPhones, down from 60 million to 65 million.
Still though, Munster said he is sticking to his $655 price target and betting that Apple will follow through with devices that will send the stock up.
"It's hard to see and imagine right now, just because there is another September quarter ahead of this where we aren't going to see much of an impact," Munster said. "If they come out with those new products, we feel great about that price target, but if they disappoint us, I'm in trouble."
—By CNBC's Cadie Thompson. Follow her on Twitter