The payments to the whistle blower did not violate any of the obligations under the proposed acquisition by Musk, according to the company.
According to the SEC filing, the social media giant intends to close the transaction on the price and terms agreed upon with Musk.
On Tuesday, shareholders will vote on Musk's takeover bid.
The sale of the company to Musk was urged by the board of directors.
The proposed acquisition was called off by Musk's legal team on Friday. The terms of the deal were violated by the multimillion dollar payment that was made to Peiter "Mudge" Zatko.
The social media company was accused by Zatko of being deficient in privacy, security and moderation.
Musk has tried three times to call the deal off.
The SEC was notified by the legal team of the cancellation of the acquisition on July 8th.
The deal should not go ahead because of the allegations made by Zatko.
In Friday's letter, Musk's legal team said that an alleged $8.25 million severance payment to Zatko from the social networking site is a violation of the takeover agreement.
The company said it has not done anything wrong.
The social media giant's legal team wrote to Musk's representatives that his September 9, 2022, letter was invalid and wrongful.
All of the conditions precedent to the closing of the Merger will be satisfied after the receipt of the approval of Twitter's stockholders at its September 13, 2022, special meeting.
The saga has become much more complex. The proposal to buy the company was first made by Musk in April. The deal was agreed to after some resistance from the social networking site.
Musk began to complain that the number of fake accounts on the social media platform is higher than what's being reported.
A trial will be held in Delaware in October to resolve Musk's attempt to cancel his acquisition of the company unless a settlement is reached first.
The allegations made by Zatko will be included in Musk's counter suit.
The matter is complicated by a Tuesday shareholder vote which could green light the acquisition.