Of the billions of dollars in customer deposits that disappeared from FTX in a flash, $200 million was used to fund investments in two companies, according to the Securities and Exchange Commission, which charged founder Sam Bankman-Fried with "orchestrating a scheme to defraud equity investors."

Through its FTX Ventures unit, the crypto firm in March invested $100 million in Dave, a fintech company that had gone public two months earlier through a special purpose acquisition company. At the time of the deal, the companies said they would "work together to expand the digital assets ecosystem."

The other deal the SEC appears to have referenced was a $100 million investment round in September for Mysten Labs, a Web3 company. In total, it was a $300 million funding round that valued Mysten at $2 billion and included participation from Coinbase Ventures, Binance Labs, and Andreessen Horowitz's crypto fund.

While FTX Ventures has done dozens of transactions, according to PitchBook, the Mysten Labs and Dave investments were the only two disclosed investments of $100 million, based on documents published by the Financial Times, which broke down how the company put $5.2 billion to work. FTX Ventures was described as a $2 billion venture fund, in its press release with Dave.

Bankman-Fried, 30, stands accused of committing widespread fraud after FTX, which was valued by private investors at $32 billion earlier this year, sank into bankruptcy in November. A central theme in the charges is how Bankman-Fried diverted funds from FTX to his hedge fund, Alameda Research, which then used that money for risky trades and loans. FTX Ventures was allegedly part of that scheme.

Neither Mysten nor Dave have been linked to any alleged wrongdoing within Bankman-Fried's empire. But the investments appear to be the first identified examples of customer money being used by FTX and Bankman-Fried for venture funding. As investigators and FTX lawyers attempt to retrace the outflow of FTX funds, these identified investments and others in the $5 billion venture pool will attract heavy scrutiny.

In explicitly linking the two $100 million investments to customer money, the SEC has raised the possibility that they'll be prospects for clawbacks. If FTX bankruptcy trustees can establish that client money funded Bankman-Fried's investments, they could pursue recovery of those funds as part of an effort to retrieve customer assets.

A spokesperson for the SEC declined to comment.

Dave CEO Jason Wilk told CNBC that FTX's investment in Dave is already scheduled to be repaid, with interest, by 2026. FTX's $100 million investment was through a convertible note, a short-term loan of cash that FTX could convert into shares at a later date. That conversion was never made, leaving Dave with a $101.6 million liability, including interest, to FTX and any successor companies, according to the company's most recent SEC filings.

"The note issued to FTX is due for repayment in March 2026," the company said in a statement. "No terms contained in the note trigger any current obligation by Dave to repay prior to the maturity date."

Wilk added that, "it is important to state we had no knowledge of FTX or Alameda using customer assets to make investments."

Bankman-Fried's investment in Mysten Labs was an equity deal. Because Mysten is a privately held company, there's no clearly defined process in U.S. bankruptcy code for clawing back those funds.

Mysten declined to comment. Lawyers at Sullivan & Cromwell, which represents FTX, did not respond to requests for comment.

An SEC complaint filed against two of Bankman-Fried's lieutenants, Caroline Ellison and Gary Wang, specified that "two $100 million investments made by FTX's affiliated investment vehicle, FTX Ventures Ltd., were funded with FTX customer funds that had been diverted to Alameda."

Irrespective of what money was being used, FTX's investments were ill-timed.

Dave shares have plummeted over 97% since the company went public, mirroring the performance of the broader basket of SPACs, which has plunged this year. In July, the Nasdaq warned Dave that if its share price didn't improve, it was at risk of being delisted. The stock currently trades for 28 cents and the market cap sits at around $100 million.

Alameda Research had previously made a $15 million investment in Dave in August 2021, before the Nasdaq listing. Dave was founded in 2016 and offers customers a free cash advance on their future income as part of a suite of banking products. Mark Cuban led a $3 million seed round in 2017.

The investment could have been lucrative for FTX if Dave's share price had improved beyond $10 a share, allowing FTX to convert at a profit.

FTX's investment in Mysten came in the midst of a crypto meltdown. Bitcoin and ether were down by more than half for the year and numerous hedge funds and lenders had gone bankrupt.

The funds were to be used in Mysten's effort to "build a blockchain that scales with demand and incentivizes growth," Mysten CEO Evan Cheng said at the time.

Representatives for Ellison and Wang did not respond to requests for comment. A representative for Bankman-Fried declined to comment.

Ellison, 28, and Wang, 29, pled guilty in New York last week to federal charges over the illicit use of customer funds for trading and venture investments, allegedly directed by Bankman-Fried. Both are cooperating with federal investigations into Bankman-Fried and the collapse of FTX.

WATCH: The terms of the $250 million bail agreement for FTX founder Sam Bankman-Fried