To create a combo route:
1) Create a new 'Route Name' entry, with a new unique route id
(e.g., you might need two of these records, to specify the two route
directions)
2) Create a new Combo Route entry attached to the new combo route
id, specifying the routes that make up this new table.
3) Add stops from the original routes to your new combo route id.
See
http://maps5.trimet.org/ttpub/timetable.config?route=Amtrak+Cascades---4
as an example of a combo route.
About merging, etc... my advice is to experiment a bit more here -- it
sounds like your merge config contains a reference to the stop you're
trying to delete...