I would like to clarify that there is not a possibility to create one Run Configurations settings for a whole Project.
In addition, I have successfully reproduced the issue when Run Configurations becomes inactive. We would investigate it further. Meanwhile, possible workaround is, as you mentioned, to open Run Configurations through another plan.
Lastly, I would like to note that if the project folder has the same name and structure as in the previous version, it would not be necessary to change the path in Main XML field after importing Launch Configuration, because the path which is specified there is not absolute path.