Here is the message I sent to Bethesda support:

I have been playing fallout 4 offline since release and had racked up 30+ hours an was level 25. My achievements were not unlocking which is normal when playing offline, however, when I got back online none of my achievements were had unlocked. I spoke to Microsoft and they give me some steps to follow.
Remove my account
Remove persistent data
Clear MAC address.

I followed these options and rebooted my game, to find my game save had been completely removed and I was right back at the beginning again. After speaking to Microsoft again they are now saying they are now saying its an issue with Bethesda.
After I reconnected to the internet I was prompted to select an option.
Console data
Cloud data (nothing saved)

I selected console data and continued playing no problem. Then Followed Microsofts advice and when I rebooted the game again it told me it was syncing data and all my saves had gone.

Please tell me you have a solution for this?
Thanks, Stephen.

Since this I restarted the game and my achievements did eventually unlock, however, I would still like to get my game save back if it is possible. Any suggestion, help and advice would be appreciated, lets face it it has gotta be better than what Microsoft told me to do lol.

Microsoft told you to delete your save.

It was likely lumped in with the persistent data, and they must have assumed you had data saved on the cloud (which you wouldn't have, as you've been playing offline for that whole save, yes?)

Yeah I had been playing offline for the whole save but once my internet was back on after moving house I loaded up the game and I guess Microsoft presumed the game auto backed up to the cloud once I re-connected.

Strange thing is there was a save available from me first leaving vault 111 which I found odd because why would that data still be available or uploaded to the cloud but the rest of the data didn't? Obviously I have raised the issue with MS and they just keep passing the blame to Bethesda but I also noticed my COD data had been deleted so its obviously what they told me to do which as caused the issue and they just don't want to take responsibility for it. Rather annoying when you have been a customer for over 8 years eh?

Yeah, but that's Micro$oft for ya. Remeber the Xbox One launch fiasco.