You won't have any trouble with AC doing this.
If you don't specify, the most likely way they'll do it is to cancel your flex booking and book a new J ticket. So your boarding pass ticket number will be different from the ticket number on your flex receipt.
If your employer isn't fussy, you'll be good to go.
But if your employer is fussy, make sure they do a change to the original booking rather than a cancellation-then-rebook.
According to some reputable sources below, what I wrote here is not accurate.