You will have to file both returns as they have 2 different EIN's. The question regarding the LLC is if it was originally treated as a Partnership filing a 1065 or if it was a Sole Proprietorship LLC. If it was a Sole Proprietorship LLC, then you would have to prepare 2 schedule C's. If it was a partnership, you would file a final 1065. You would have to allocate the two by the dates before and after the change-over. The software will not do the allocation, you will have to do it either using a bookkeeping software or spreadsheet.
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