OK been playing around with a new linkstation live 1tb with PS3 60GB and have found a temporary workaround for missing content issue on the PS3.
First you need to refresh the linkstation database
1. Create a new share on the linkstation (keep this share empty)
2. Disable the media server and then point it to the new empty share, tag reinitialize the database and select refresh now.
3. When server comes back up check on the PS3 that all content has been removed (3-5 mins).
Now to get the content back
4. Disable the media server and point it back to your original share (ie where your media files are located)
5. Tag reinitialize database, and select refresh now, but also change the refresh interval to 600 from the default.
6. Now wait for several hours. I have alot of media files (around 400gb of .mp3, jpg, mpg) and it took overnight to refresh the database fully). Note you will need to ensure that the power switch is set to on and not auto during this process.
After three days of messing around I managed to get all of my content on the PS3. Hope this works for others.