After having tried to analyse the bug an several backups (unfortunately
they took 2-3h each), I ended up that the bug completely disappeared.
Please don't ask me why...

I uninstalled backintime, deleted all configs, deleted the backups from
the NFS drive, reinstalled backintime, didn't put ".gvfs" in the exclude
list and now everything works fine. No ghost files/folders etc.

Sorry that this bug can't be traced... I can send you the logs I have,
but since the bug didn't appear anymore they will not help you. I have
no idea how to proceed... Any ideas?

-- 
Deleted Files are stored in snapshots forever
https://bugs.launchpad.net/bugs/406092
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Status in Back In Time: Confirmed

Bug description:
The classic example of this is when Back In Time backs up your desktop.

For example.

I create a file called 'foo' on my desktop to write some quick notes in.

I create a snapshot, and '~/Desktop/foo' is now stored in 'Snapshot1'.

I delete 'foo' from my Desktop, as I no longer need the file.

I create another snapshot 'Snapshot2'. 'Foo' is still listed in 'Snapshot2' as 
a file (although obviously it hasn't changed). 

For each snapshot that is taken after this, 'foo' will always be listed as a 
file in the snapshot, and never removed from the series of backups.

What should happen is, 'foo' should be stored in 'Snapshot1', but should not be 
stored in 'Snapshot2'.

When 'Snapshot1' is deleted (either manually or automatically), 'foo' is no 
longer backed up through back in time, as it no longer exists on the system.

The only current workaround I have found, is manually deleting the files I want 
to be removed from snapshots, so they are not included in the next sync.

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