The bootloader update should not be needed, except for CC3D or Atom boards flashed using the old v3 bootloader.
Bootloader version 4 is needed for CC3D/Atom or automatic reboot do not work correctly and vehicle wizard will fails.
Download the appropriate bootloader and go to the Firmware Rescue page.
Please note all the files above are bu_[BOARD].opfw, if you plan to flash a .bin file the DFU method or ST-Link method should be used.
Unfortunately, the CPU used on the CC3D flight controller does not support the DFU bootloader, see this page for flashing bootloader using a FTDI connected to the main port. Note that the page seems to be unviewable now and you may need to view it on archive.org.
There is three ways to update or flash a firmware: