I don't know the answer to your question for sure. But off the top of my head, since you operated the LLC with a different FEIN than your sole proprietorship, my recommendation is to file two different Schedules C. This should prevent the IRS from sending you a CP-2000 letter down the road due to mismatch of 1099-NEC and 1099-MISC you may have received under the other FEIN. There is no harm in filing two Schedules C. If you don't have accurate breakdown of expenses, I would just use a reasonable allocation between the two Schedule C. Since it doesn't change the tax liabilities, the IRS shouldn't care. IRS agents I've dealt with are quite reasonable.
