our non-profit owns. We have a contract to sell it but do not want to incur capital gains. Can we transfer the deed to the national headquarters for our non-for-profit that has a tax exemption and let them complete the sale? (the buyer would agree). Also, should we file the missing 990EZ's now. How likely is it that the IRS will come after us after we dissolve and require us to pay late fees for failing to file the 990 EZ's?
I would suggest contacting a business/ tax attorney in the Chicago area as this could get quite complicated. There may be other issues that you as a director need to address. Look in the AVVO directory for some good attorneys in your area.
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Real Estate Attorney
You are governed by the doctrine of "cy pres" meaning, you have to give the profits to a similarly situated organization with a similar mission and 501(c)(3) status. The fact that you are part of a larger organization indicates that you may be obligated to let them administer your dissolution. Definitely get competent counsel to help. When in doubt, ask the IRS, they do issue opinion letters.
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First, you should consider immediately filing your 990 EZs and filing for tax-exempt status again. It is possible you could get your new favorable determination letter from the National Office of the IRS quickly enough to save the sale for your group, which would be nice. That would especially be the case if you can get on the phone with someone at the National Office and ask for help. We know people at the National Office, and I am sure a good tax lawyer in Chicago will as well. Also, a good tax lawyer in Chicago will know with whom they must talk at the Attorney General's office in the State of Illinois so you are also re-qualified with the state.
Second, yes, it might be enough to make a liquidating transfer - as suggested by one of the other fine people who responded on AVVO - to the National Headquarters of your organization.
Third, if your organization has no assets, then there is nothing for the IRS to come after.