Cotten, 30, died in India last December from complications from Crohn's disease, according to the company.
Users have been complaining about "withdrawal issues and a lack of communication" from QuadrigaCX for months, CoinDesk said.
"The transfer of coins from the cold wallet to the hot wallet was performed manually by [Cotten]", the affidavit from Robertson states.
Jennifer Robertson, the widow of the deceased founder, suggests that Cotten was the only person in the firm to have access to funds and cold wallets and no other person had any knowledge of the same.
"After Gerry's death, Quadriga's inventory of cryptocurrency has become unavailable and some of it may be lost", Robertson said, adding that the company's access to currency has been "severely compromised" and the firm has been unable to negotiate bank drafts provided by different payment processors.
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While Robertson has Cotten's laptop, it's encrypted and she does not have a password or recovery key.
Cotten allegedly held "sole responsibility for handling the funds and coins" for an exchange that boasts roughly 26,500 Bitcoin ($92.3 million USD), 11,000 Bitcoin Cash ($1.3 million), 11,000 Bitcoin Cash SV ($707,000), 35,000 Bitcoin Gold ($352,000), almost 200,000 Litecoin ($6.5 million) and about 430,000 Ethereum ($46 million), totaling $147 million.
"Despite repeated and diligent searches, I have not been able to find them written down anywhere", the affidavit states.
A statement from QuadrigaCX's board of directors said: 'For the past weeks, we have worked extensively to address our liquidity issues. "I'm kind of preparing for the worst".
In a statement posted on its website on January 31, QuadrigaCX said that it applied for creditor protection in the Nova Scotia Supreme Court "to allow us the opportunity to address the significant financial issues that have affected our ability to serve our customers".
Robertson has retained an expert to try to access the funds but he has so far not been able to do so. She said she had also received threats and slanderous comments.