I believe if you miss your outbound, your ticket will be canceled (according to whatever refund class you paid for -- I'm assuming you're talking about a non-refundable ticket).

What about this though... Book the cheap ALB-SJC ticket, and if it looks like you aren't going to make that flight, call and change ($100 change fee) your outbound to EWR-SJC.

You'd have to do the math to see what kind of gamble/payoff this method results in (I guess you'd end up with a very expensive EWR-SJC last-minute ticket, so it might not be worth it). But it's something to consider, anyway.

What about just booking EWR-SJC with a return to ALB? That might get you half the savings.