I believe I have found a solution to this particular issue - it is unique to our environment hence why there hasn't been any activity around it in any forums but in case anyone else comes across this thread the solution is quite simple in the end.
In our environment we have a few processes blackholed via group policy into svchost as a way to eliminate execution - this policy includes reg.exe.
The key is located below:
Computer\HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Image File Execution Options\reg.exe
FSlogix must use Reg.exe during it's process somewhere - by blackholing this service we receive the error about the rename of new export which in turn affects the users existing profile. The profile resorts back to a blank empty profile and any changes are not saved.
This has been difficult for us to determine as only a subset of users have this blackholing in place - once one of them log in the symptoms begin so it appears intermittent.
By removing the blackholing on this file to SVChost the FSLogix profile handling occurs as normal - however if the profile was logged into with reg.exe blackholed then that profile is damaged - restoring to an earlier date before logging in restores the users profile.