Adam,
When editing InRoads generated graphics, you must be aware that certain graphics contain "user data" that adds intelligence to those objects. In other instances, we add graphics such as in the case of profiles and cross sections. These are text nodes that tell InRoads what the graphics are and define the data required to make them intelligent.
As a general rule you should be ok editing InRoads data. If you copy or delete or modify the graphics that compromise this data you could cause some issues.
HTH
Thomas