Steps to "fix" the issue:
1) enter the top-level group (select, 'Ctrl+Enter')
2) use <Tab> to cycle through the content of that group
3) read the messages in the status bar and stop cycling when message says '3D Box'
(it's the first group selected with <Tab>)
4) apply menu 'Path > Object to path' (or 'Shift+Ctrl+C')
(this will convert the 3D Box into a regular group)
5) leave the group ('Ctrl+Backspace')
6) apply 'File > Cleanup Docment'
7) save
Now copy and paste of the top-level group works as expected.
Steps to "fix" the issue:
1) enter the top-level group (select, 'Ctrl+Enter')
2) use <Tab> to cycle through the content of that group
3) read the messages in the status bar and stop cycling when message says '3D Box'
(it's the first group selected with <Tab>)
4) apply menu 'Path > Object to path' (or 'Shift+Ctrl+C')
(this will convert the 3D Box into a regular group)
5) leave the group ('Ctrl+Backspace')
6) apply 'File > Cleanup Docment'
7) save
Now copy and paste of the top-level group works as expected.