While the business was a single-member LLC, it could qualify as a "disregarded entity" that files Schedule C. Once the LLC added a second member, it defaulted to a partnership for tax purposes, and was required at that point to file a Form 1065 partnership tax return.
Essentially, you have been filing your tax returns as if you had a Qualifed Joint Venture. Because the company was an LLC, however, you were not eligible to report your income as a qualified joint venture.
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