How will it affect current routes that are setup as a Loop Route?
Routes that have been already setup as a Loop Route will have the stops listed in the order of the first loop and and then from that point repeat or loop stops will appear in the order of their departure times.
For example, if a route has stops A, B, C, D, E in loop 1, and then in loop 2 the same stops have been entered as A, B, C, D, E - but departure times have only been entered in Loop 2 for stops B and C, the route will look like this:
A, B, C, D, E, B, C
If Stop C on the 2nd loop has a departure time earlier than Stop B, the route lineup will look like this:
A, B, C, D, E, C, B