After a little more digging, i found this interesting comment by John Gordon, the suggestion in simple terms is to reset the iPhone and restore immediately, followed by a re-sync.
Full instructions can be found on Johns blog here: http://tech.kateva.org/2008/09/iphone-21-does-not-fix-unknown.html .
This is done using the latest version 8 iTunes and iPhone firmware.
So far, so good, all data is back, unfortunately all the icons have been repositioned, its a shame apple can’t retain the position of the icons. Data and passwords seem to have been retained.
Everything seems updated, so this is probably the best solution at the moment, i’ll give some more feedback after a few applications have been updated. The true test.
[UPDATE 20th Oct 2008]
Looks like this has worked, i upgraded 5 applications over the weekend, everything is still working correctly.
[UPDATE 28th Oct 2008]
All still working fine, more updates have been aplied – looks like this does resolve the issue.
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October 16, 2008 at 7:44 am
bumbleit
One side effect of performing the reset, was that my AppStore icon on the iphone indicated that there were a number of applications that required an update.
Given I updated everything after the restore, I expected the updates to cancel themselves out at some point. As of last night, they were still shown. So I manually installed each update, which all seemed to go through fine.
This morning, when connecting back to my PC, I had another update to the AirSharing application, which I suspect had already been applied. I installed anyway, half expecting it to fail.
However, everything was fine.
It’s now 10 days since the restore, and everything seems to be going well. Fingers crossed, it may actually have fixed the problem.