I had a very similar situation with my standard poodle puppy Jet and my elderly giant schnauzer Cas. Cas let the little puppy do whatever he wanted, but then the puppy wasn't so little anymore and suddenly one day when the puppy went in to boisterously play as usual, Cas just about ate him. (Luckily Cas has good bite inhibition so he didn't actually leave a mark on the pup, but if he were an impulsive dog he could have done real damage.) After that, Cas was snarly and annoyed by the very sight of the puppy for a good couple months, and I was worried I was going to have to keep them separated indefinitely, as the size difference made disagreements especially dangerous (Cas is about 100 lbs when fit, and the puppy was about 35 lbs at the time).
Luckily it all worked out - the puppy grew up and developed some manners, and now they're buddies again - but in retrospect I should have nipped those behaviors in the bud and not let the situation escalate in the first place. Jet is 15 months old now so he's still pretty hyper, so I make a point to not let him badger Cas, because I want them to stay friends. I just call Jet off or redirect his behavior (e.g. giving him a toy) if he's being too rough or persistent with Cas, and if that doesn't work, I give him a little time-out to settle down.
Luckily it all worked out - the puppy grew up and developed some manners, and now they're buddies again - but in retrospect I should have nipped those behaviors in the bud and not let the situation escalate in the first place. Jet is 15 months old now so he's still pretty hyper, so I make a point to not let him badger Cas, because I want them to stay friends. I just call Jet off or redirect his behavior (e.g. giving him a toy) if he's being too rough or persistent with Cas, and if that doesn't work, I give him a little time-out to settle down.