First, I do not understand the reason for the fear of applying. Your BigCo employer should not treat it any different than your applying to another BigCo. They are not going to care (much), people explore other opportunities all the time.

But acceptance to YC is an all or nothing deal. They fund teams and would generally not fund a company that lost a key cofounder between acceptance and attendance. That's why they ask you to commit. Thus you should be upfront with your cofounders that you might not attend, which will likely void the acceptance (which, I guess, would greatly demotivate them). My 2c.