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To operate an LLC in two different states you will need to have a filing of a "foreign entity" for the state where the LLC is not originally organized. In your case, you are organized in New York, and you need to file as a "foreign entity" in Virginia. Once you have done this you can request a certificate of good standing from both states (you can already request one in New York).
I already registered the LLC in Virginia. Is "filing of a "foreign entity"" in Virginia a different procedure.
No, that is the same process I was talking about. If you are already registered, you can simply request a certificate of good standing from the Secretary of State. This simply means that you have paid your annual fees, there are no regulatory violations against your business, and that your business is still allowed to conduct business in the state.
You can find the appropriate forms and fees here: http://www.scc.virginia.gov/clk/copy.aspx
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