I cracked it. I had to use a jack-hammer tho.

I deleted all the entries in the Files table associated with the problematic portal. I think accessed the File Manager (which worked without throwing the error this time) and re-synchronised the File System.

I believe the problem was with files that belonged to paths that had the %20% character that had been added in previous 3.x versions. Those characters might have started to cause problems with the changes to the File system introduced in 3.3.x and 4.3.x.

So- all is well that ends well.
Unfortunately however this unavoidably broke all the associations in Media and Documents modules. So I have some work to do on those.

I hope this helps anyone else experiencing this problem.
Cheers,

Scotts solution fixed the Host's file manager for me but not the Portal's file manager.  Guess Im stuck there.  Wonder why not everyone is experiencing this.  Is the mothership running on 4.3.3?

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