I don't work in a bank, but here my thought, based on what I know. Correct me if I'm wrong.
Normally, at least at the credit unions (and probably banks too), they order only the paper money they have to have for their normal operation. They try to keep the least inventory of notes as possible, in order to have to pay the minimum transportation, insurance and storage fees (to make bigger profits!). In the case of 100 $ notes, in my opinion, it's only in the big branches with a large note rollover they could have a brick of 1000 notes (100,000$!
) ). In the smaller branches, they could need to have only a bundle or two to cover their needs.
As the BoC recalls all the old 100$ notes, it's possible that the banks (and credit unions) will get the same number of new 100$ notes to compensate. So it shoudn't have any shortage in these notes.