When you create an cl file , you choose :
cl-data - output - nc-sequense (or operation , or set ) - then you choose your sequense. The next menu that shows is the one whit default set to display (i guess this is where you normaly choose file ???) In that menu there is an option called mirror . So instead of choosing file , Click mirror , then you have to specify mirror plane and then your back to the same menu again where you choose file this time , and the cl-file will be output mirrored. (if you want you can look at the file by coosing display , so you will se that the result is what you expected!!!!)
This works in Pro/E 2001 anyway.......
Regards/ T