Hello macbahi,
First Question:
I see the issue you get, and it would be good idea to have the possibility to change the .scs when using "save as" or "Project Rename". Unfortunate this is not done, but I will add this to the PLUS+1 GUIDE wishlist.
The solution to your problem is to change the name of the .scs file in the PLUS+1 GUIDE when opening the new version of the application.
The image (RenameSCS.png) shows where you can change the name of the .scs file.
Second Question:
The "Value" column in PLUS+1 Service Tool is the name of the application, or the application ID to be correct. This can also be changed in PLUS+1 GUIDE.
The image (ApplicationID.png) shows where you can change the name of the application ID.
I hope it helped.
Have a nice day.