To answer your question, unfortunately, although you have some options, the IRS will receive on the Company's 1096 exactly what was reported to you on your 1099, so even if you adjust it "accordingly" on your end when entering the information, the IRS will likely process your return, but in time send you an "adjustment letter" charging you for what they see on their end the "short payment" of taxes on your part. You could wait on filing and insist that the Company send you a corrected 1099, but it sounds like you haven't had much luck at all with them thus far. Check closely with the original agreement you signed prior to depositing your funds into the account to see what the fine print says.
