There was a bug, recently fixed (although there has been one post that may cast some doubt on this), that caused problems when the primary route was smaller in size than the secondary route. My practice has always been to make sure that the larger route (the primary route) is loaded first and the smaller route (the secondary route) is merged into it so I had never encountered this bug.
When the merging process reports a conflict between layer names (i.e. both routes have a layer with the same name, usually the "route-layer" from each route) the layer names from the primary route will be shown above the layer names from the secondary route. You will be given the options of solving the name conflict by:-
- performing a merge of the conflicting layers,
- deleting one of the conflicting layers, or
- renaming one of conflicting layers
to allow the merge operation to proceed.