Hello tadk,
There are no permanent routes that are being made on the board, so you
do not need to do anything special to clear them. These settings are
local to the task in the program and will be cleared whenever you clear
the task.
Also, to provide some clarification on your previous comment, the PFI
lines are simply general-purpose timing and triggering lines. Each pin
on your board has a physical pin number and then a terminal name. The
physical pin numbers are there so that you can make the proper
connections to your terminal blocks. The terminal names, such as PFI1,
describe what functionality that physical pin has on your particular
board.
Anytime you see reference to a PFI line, it is referring to the terminal name which describes a particular timing/triggering line. It is not referring to an actual physical pin (since these can vary by device), or to an internal route. Of course you can route signals to a particular PFI line, but the PFI name is not referring to that route.
I hope this clears things up for you a bit.
Best regards,