As long as you can sell the house and the lot it sits on for enough to pay off the existing mortgage, I don't see it being a problem with the mortgage company. However, you will have to be really really careful with the paperwork because it would be really easy for a mistake to be made and both lots accidentally sold to the purchaser, or the bank accidentally not releasing the lien on the second lot. You will also have to be really careful with your disclosures if the property looks anything like one big lot rather than two.
Your mortgage may have both lots on it but I'm sure it is recorded as two properties by the County tax assessor. If they are both conveyed on one deed, you can have a title company convey them in to two separate deeds as long as there aren't any local restrictions saying they can't be split. As long as there is a separate deed for the lot you would like to sell, you can sell it separately.
Conveying it isn't so much the problem as making sure that there is no security instrument lodged against the property you're trying to sell. As Ldij says, no sane purchaser would by a property that was encumbered by someone else's lien. Further, if you make any representations (warranty deed, for example), you could be into financial heartaches if you don't take care of this first.