Yeah you can't expect them to handle you bioload 100% when a lot of your beneficial bacteria is obviously living in your canister filter and that suddenly gets cut off. Your bacteria colony only grows to the size of its food source--your bioload. Cutting off half of it suddenly is going to give you a mini cycle no matter what the situation.
Does that mean they can't handle a large bioload given time by themselves? No.
I would bet they did a whole lot better by themselves than if you had no backup at all.