You are correct that the classification in the return is what the government sees, but the document header is what the law (Rule 53) and your customers require. A Credit Note titled "Tax Invoice" is a compliance error. You should update your Tally print settings to ensure the header matches the "Nature of Document" to avoid disputes with customers and the tax department.
You can use Form 26A to avoid paying the ₹96,652 TDS amount since the builder has already paid tax on that income. However, you will still be liable for interest (1% per month) and late filing fees (₹200/day). It is recommended to consolidate installments by Financial Year to minimize penalties. The process is electronic and requires a CA-certified Annexure A.
You can either cancel the bill via a Credit Note and issue a fresh one at 18%, or simply issue a Debit Note for the 13% GST difference. The Debit Note is usually the more efficient legal remedy for short-paid tax. Note that interest will be applicable on the tax difference from the original supply date.
To regularize, you must first file ADT-1 with additional fees to put an auditor on record. The Auditor must then sign the pending Balance Sheets and generate a UDIN at the time of signing. Once AOC-4 and MGT-7 are filed for all pending years, the company becomes eligible for a Strike-Off (STK-2) application.