I updated after putting it off for so long from 5.0 -->5.2 --> 6.02.
No major issues except the data volume was not available in 5.2.
I could see that it was fine data wise in the OS so I just continued with the update and once in 6.0.2 all was good.
All applications, users and settings was 100% functional. I'd already bought a PCI-e USB card for the UPS and this worked fine too.
I'm now on 6.0.2 update7 on both my N54Ls and the 4Tb USB HDD I used to backup my primary data is now in the secondary after removing it from the case.
I also have a remote ESXi 6.0.2 DSM which I copied over my data to using USB and after a bit of messing around have the Shared folder replication working.
Tip - If you want to preload your data, DSM will want to ignore it so run the sync script and allow it to create the new shared folder on the destination, cancel it on the source then delete the new share e.g. photo. Rename your shared folder with prepopulated data from photo_1 to photo, re-apply share and file permission including resetting on all subfolders and files then re-run the sync task and it should now work and take a fraction of the time it would have.
This also works if you want to have a shared folder on volume 2.