It seems most likely that you are opening a new empty scenario instead of the existing scenario you think you are opening. This is quite easy to do with the current version of rsyncrosim, as the library, project and scenario functions automatically create new objects if the one you specify does not exist.
The best way to see what is going on is to check the summary contents of each object after you load it, to make sure it is in fact what you expect:
project(Lib, summary=TRUE) will list all the projects in library Lib
scenario(Prj, summary=TRUE) will list all the scenarios in the project Prj
You can then confirm you are referencing the correct project and scenario before actually opening it.
I hope this helps. Colin