After having checked the problem, the solution was/is as follows:
The Eclipse project was created by importing an exisiting project from the file system. ...and: there is a little checkbox in the import dialog: "Copy project into workspace". If this is pressed then Eclipse does not work on the directory which was created by the CaptainCasa toolset, but the directory was copied into another location.
As result the Layout Editor still takes the original directory it created, whereas the programming is done in the copy created by Eclipse.