I wanted to share a serious problem for us.
When recomposing the linked-clones, the users would lost all the settings. (Outlook, Desktop icons layout, icons taskbar, etc.)
After several days of testing, we concluded it was caused by our script customization.
Yesterday, I found out the problem: we inject some keys into default profile ntuser.dat (C:\users\default\ntuser.dat).
It seems touching the default ntuser.dat makes resetting the ntuser.dat of the persona profiles.
When it occurs, in the persona logs, there are no log about ntuser.dat being retrieved from Persona.
The local profiles aren't affected to this issue, but the roaming profiles are.
Edit: Even copying a file .config into the default profile, it does the same behavior...
Hopes it helps someone.