The problem with uneffected changes in the structure attribute resolved itself.
I still have a major issue on the debug part. Even after I 1CP (F5) and run the debug mode (F6), The content of the PTA does not reflect to the content of the previously published area. Note that the public area is correctly updated by the 1CP.
Trying to remove the test folder from the platform server directory, only temporarly solve the problem. I can debug on the public area, but this is not a desired approach for me.