USA Tax questions about temporary relocation for work

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The company I work for is based in New York City. The company made the decision to open a satellite office in Chicago, and I volunteered to move from New York to Chicago to help open the new office (with the assumption that it would be a 6 month assignment, after which I would return to New York City).

The company rented an apartment in Chicago (the lease began on March 15, 2011). Since the lease on my apartment in New York City ended on March 30, 2011, I decided to not renew the lease on the New York City apartment in order to avoid paying NYC rent while I was away in Chicago. I moved into the company-paid apartment in Chicago on March 26, 2011. I packed up all of my belongings into a truck and everything I own is currently in a storage unit here in Chicago (which I pay for, and the company does not reimburse me for it). The company did reimburse me for all moving costs including the truck, gas, boxes, movers, etc.

So, to summarize, I lived and worked in New York City from Jan 1, 2011 to March 25, 2011. I have since lived and worked in Chicago from March 26, 2011 to today (November 19, 2011). I was supposed to return to New York City already; however, the assignment was taking more time than expected and we mutually agreed to extend the temporary assignment until January 15, 2012.

In the past week, the company and I discussed that the assignment is still taking longer than expected, it was proposed to extend it again until the end of April 2012. However, the company's accountant is saying that if I stay in Chicago past the end of March (signifying a full year), that I will be considered a permanent employee in Chicago, and that there may be tax implications. The company is also saying that the will not continue to pay for the company apartment past the end of March.

Finally getting to my questions: I'm wondering if the company is just being cheap (not wanting to pay for the apartment anymore), or if there are legitimate reasons for them not wanting to extend this arrangement past the end of March 2012, or perhaps they're trying to nudge me to return to New York City sooner than I'd like. If I want to stay until the end of April, what are my options? Paying the rent out of my own pocket is not my preference, of course. Perhaps I could pay for it and expense it back to the company rather than them paying it directly - or is that the same thing?

Also, based on these circumstances, what should I expect to happen when I go to file my 2011 taxes? Will I have to file as a partial year resident in New York City/State even though I only lived there for 84 total days in 2011? I am not sure what my "tax home" will be, etc.

Any advice or guidance that could be offered would be greatly appreciated. I'm considering hiring an accountant for the first time in my life (my finances are not that complicated), but before I do, I'm trying to gather as much information as I can.

Thanks in advance!
 

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