if you sold the assets as opposed to your stock the S-Corp must file a final return and it is the one that reports the gain or loss on the sale of its assets. as noted the S-Corp would need to file form 8594 which details the allocation of the sales price which the IRS will match to what the purchaser reported. if there is a difference you can expect that the IRS will audit.
hopefully, there is a written agreement because that will prevail. if not the IRS will likely take both owners to court where they can argue as to what was agreed to and the judge will make the final decision unless both parties agree to an out-of-court settlement.
https://www.irs.gov/pub/irs-pdf/f8594.pdf
https://www.irs.gov/pub/irs-pdf/i8594.pdf
