The first report, issued by Ban's office on Friday, made no mention of the Polisario's proposals for a referendum - suggesting that Morocco's plan for the region's self-rule was the only one under discussion.
The new report addresses this, removing a number of paragraphs.
Morocco has proposed limited autonomy for the territory, with it remaining under Rabat's sovereignty, but the Polisario Front has demanded a referendum that includes the option of full independence.
No country currently recognises Morocco's rule over Western Sahara.
Paragraphs removed
In his original report, Ban recommended the Polisario "could be asked to test Morocco's readiness to take part in serious, constructive negotiations" by making "concrete proposals to clarify or amend Morocco's limited autonomy proposal".
He also said: "If the negotiations are to lead to a positive outcome, both parties must recognise that the question of sovereignty is, and always has been, the main stumbling block in this dispute, and that it is in this highly sensitive area that a solution will need to be found."
These paragraphs had been removed in Monday's report and it was made clear that the UN Security Council had requested Ban's office arrange for the talks "without preconditions" and with a view to achieving a "lasting and mutually acceptable political solution".
But UN officials would not say whether they had discarded the concept of negotiating on the basis of Morocco's plan.
Instead, a UN statement said it was "in the best interests of the process" for Peter van Walsum, Ban's special envoy, to brief the Security Council orally next week "rather than in a public report."
The two sides met in June, the first meeting in seven years, for two days of UN-sponsored talks aimed at ending the 32-year-old dispute over the Western Sahara, a former Spanish territory.
The area has a population of just 260,000, but has phosphate reserves, rich fishing grounds and is thought to have oil.
Many thousands of its people live in refugee camps across the border in Algeria.
The United Nations brokered an end to a low-level guerrilla war in Sahara in 1991, but no political solution has followed.
Negotiations are set to resume in the US on August 10 at the Greentree estate in Manhassat, Long Island.