As gfunkdave mentioned you checkin once and can reprint BP many times without affecting the checkin time stamp.

However the OP situation has to do with putting the flight under gate control within the RES3 system at AC (UA legacy had a similar procedure and it is common on most passenger service systems). When the flight is placed uncer gate control, only the gate agents have access to edit flight information and passenger lists, including printing boarding passes. After the flight is under gate control all other employees lose edit access rights until either the flight departs or is cancelled.

There is an over ride available for supervisors, the supervisor can take the flight out of gate control and place it back into operation for checkin purpose. At smaller stations, the checkin supervisor calls the gate and tells them that gate control will be removed for 1 minute to handle the specific situation. This only works a smaller stations (think YQR, YXE, YEG, YLW. YYJ, etc) as the airport employees all know each other and are not under constant tight deadline situations.

At larger stations (think YYZ, YVR, YUL, YYC) the supervisor override is still avialable but local custom is that it is never used. If the checkin supervisor completes the over ride without Duty Manager approval, they can expect to be in the General Manager's office for some explaining.

Also I should point out that in todays checkin and gate environments, it would not surprise me to learn that AC Corporate IT has removed the ability for supervisors to pull flights from gate control. Therefore all stations are on equal footing.