I'm pretty sure I got switched to FedLoan before I actually certified any employment (I could be wrong, but that's what I remember). And I saw those stories about loans going into deferment instead of counting, but I haven't had any particular problems with FedLoan.
IIRC the issue is that you have to be paying under an income-based repayment plan for the payments to count toward PSLF, and if you don't recertify your income on time (once every 12 months at least) you'll lose a month because they'll stick you on the standard plan until the certification comes through. Also, if you change your payment plan (like from IBR to REPAYE) it can take them a little while to process the change, and you can lose a payment that way. That is, once you request to change your plan you're off the old plan, but if they don't get the change processed by your next payment due date, you're not yet on the new income-based plan, so that month you'll be on the standard repayment plan, which won't count toward PSLF (you can defer if you can't afford it, and I think they let you do one month with a $5 payment, but still counts as standard). You do kind of have to stay on top of everything, but I don't know how specific that is to FedLoan.
Edit: deleted the bit above that was wrong - see below.
(FWIW, I've only certified jobs I've left - clerkships, so short term - because my theory is why bother having my employer certify until I know how many years I've done with them? A friend in my office takes the opposite tack, and certifies her employment every year because she's afraid something will happen and some of her years will get lost. But since it's literally just your employer giving your start and end date I don't see how that can really happen, so I don't see any issue in waiting if you don't want to certify now.)