The other possibility is that the other programmer discovered some kind of technical hurdle that was high enough to sink the whole project, and he figured there

The other possibility is that the other programmer discovered some kind of technical hurdle that was high enough to sink the whole project, and he figured there was no point in hanging around any longer. If he communicated it to the math guy and the CEO, they could have very likely brushed off his concerns in their overconfidence. Anyway, the programmer abruptly leaving is a sign of potential trouble.