If you power on the Roboclaw and the three LEDs are cycling it is already in bootloader mode. The popup screen is a general message and doesnt apply in your case.
If the three LEDs are cycling and the unit is showing up in Basicmciro Motion Studio(please make sure you sare using Basicmicro Motion Studio and not the old Ion Motion Studio), then clicking the firmware update button should start the update and it should take no more than a few seconds. If nothing happens or your still get the popup there could be something wrong with the USB connection or the power source.
Note, you must power the Roboclaw from an external power source. It is specifically design not to run from USB only power(though some still can bleed through).
I recommend shutting down everything and restarting and then Connect the Roboclaw to the PC, open Basicmicro Motion Studio, waiting for the board to show in the device list and the clicking update firmware. If it doesnt complete quickly(maximum of 10seconds) its not going to. At that point I recommend you call in to us. There may be somethihng wrong with the Roboclaw. If that is the case we'll have you send it back and we'll test it and replace it if necessary.
P.S. Never wait hours to restart a device, its an old wives tail or an excuse some people use to get you off the phone(not at our company
). It is a complete fabrication that anything could take an hour or more for some magic to happen during power off. The only reasonable delay in power cycling is waiting for power caps to discharge which can take some time on some electronics(minuts, not hours, not on any consumer device I have every seen). In general you only need to wait till the LEDs turn off on a Roboclaw after disconnecting power before you can power it back up.