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Send Realtime SysEx setting on the FM3 / AxeFX3 needs to be turned on.
Turning On/Off effect blocks on the AxeFX III
On the AxeFX III, go to Setup >> MIDI/Remote
Navigate to the Bypass tab
Assign a CC number for each specific block. A CC value of 127 will engage the block, and a CC value of 0 will bypass the block.
For example, I have Drive 1 assigned to CC#4. If I send a CC#4 value 127 message, it will engage the Drive 1 block. If I send a CC#4 value 0 message, it will bypass the block.