[micecof]

Our intention is not to recover the 13 weeks of pay, but we would rather let them keep it, and remove them from the company being that's the "pay out" they get for their shares.

Although, we are trying to understand if this could be considered as fraud so we can remove them with a legally solid reason, and confiscate their shares.

[gnicholas]

Sounds more like embezzlement than fraud, but a key question will be what powers the CEO that don't require shareholder votes. For example, if an employee came to him and asked for 2 weeks of pay advance due to some emergency, could he grant it unilaterally? Obviously it's different since there's a conflict of interest when he's doing it for himself, but it's still a relevant data point. Check your bylaws to see if this sort of thing is spelled out.