Was this covered in the letter of intent? If this is the first draft, it should be able to be negotiated, but realize that the valuation should change, based on a reduction of assets included in the sale. Be prepared to extend the negotiation period by possibly quite a bit of time, or a rejection. This is why it is so important to review all aspects in detail early in the discussions. Good luck. Do you have a good business lawyer on your team? The accountant is good for financial review, but a lawyer is needed to protect your interests.

It is all a matter of negotiations with the buyer.
The straight forward way is if you add a clause that you can use and resell the software with a perpetual license. This way they will have the software, but you will be able to use it also. This is the most neat and clear way to do it with just 1 paragraph. This is what I advise you to do, unless you see a risk of the buyer also having the software.

If you want to have exclusivity on the software, its another story. You should clearly understand how this software is booked as an asset. If its one of many, among software production, and you have not made a clear valuation, the 1M you stated is just an assumable figure. If you want this software to be left for yourself exclusively, you should be careful of public statements of valuation, or you will risk losing this value on the deal, if you exclude it.
To exclude it from the acquisition, you will have to exclude it from your balance sheet, e.g. you can sell it before you sell the company. You can sell it to yourself or another company for a nominal value.

Please provide more details, if you want further advise:
- Are you sole(single) owner?
- Why your accountant says its too late, when you haven't signed the deal yet?
- Did the buyer agree to exclude this software from the deal, or you want to do it without his consent?
- Did the buyer buy the business, knowing about the software?

1. Your accountant is not the person you go to for Legal Advice. 2. Unless the purchasing agreement is signed by Both Parties it can still be amended. 3. The prospective buyer may have submitted a template purchasing agreement they obtained online. Have an attorney who specializes in business law review and amend the agreement to protect your intellectual property and to maximize your price. You can sell your company once, so don't risk cheating yourself. Get legal assistance.

Selling your software is completely your decision, if you sell your business and 99% of it is dependent on your software, selling the business without it will be loss for you. Besides if it is less than 50% of the business you can negotiate it with your buyer.
You can use these links if you are serious about selling your publishing business: https://www.businessbroker.net/keyword/magazine-and-publishing-businesses-for-sale.aspx
https://www.businessesforsale.com/search/publishing-businesses-for-sale
Besides if you do have any questions give me a call: https://clarity.fm/joy-brotonath