For the G28 commands you can simply move the machine to a safe position where the limit switches aren't triggered and send the G28.1 command. Then when it reaches a G28 it will move to that point, but it will no longer trigger the limits.
For the M6 command you only have 2 choices. First, delete them as described, or second, use an interface that ignores the M6 or "changes" the M6 to something else, like an M0 program pause command.
Aside from the above you could see if you can edit the fusion post processor to not put those in there.