What should I do?
Don't get intimidated, don't sign/accept/submit to his "agreement" now that you are securing employment elsewhere, and make sure that henceforth all your communications with the CEO & his startup be --or continue to be-- in writing.
The CEO's attempt to be reimbursed is pure non-sense because hitherto there is no mutually agreed clause between you two to that effect. Generally speaking, compensation is for the professional's work, not for his employment spanning "n" pay periods. Having there been no employment/founders agreement of any type, he will be unable to prove that this was agreed any differently in your case.
Furthermore, the CEO's threat to seek reimbursement of your earned compensation unless you submit to his "mutual" agreement not only amounts to extortion, but it also reflects his cluelessness about contract law. For instance, that contracts which are signed under hardship or duress are voidable.
By contrast, submitting to his conditions will needlessly impose on you the burden of proving duress once you decide the situation is unsustainable. This is in addition to the legal weight with which your acceptance and subsequent conduct would support the CEO's allegation(s) that you two have "at all times" been in a cognizable contractual relation.
Being realistic, it is highly doubtful that a startup which pays you weeks late is able --or even willing-- to spend money on a lawyer for nonsense like this.