Just having experienced this problem myself I did some research and
apparently changing $Conf{TopDir} after installation is not supported as
stated by the README.Debian for BackupPC:

-- 8< --
If you do not like the default data directory (/var/lib/backuppc/), you
should move this directory where you want and make a symbolic link from
the new directory to the default one (all paths are hardcoded so it's the
easiest way to change the data directory).
-- 8< --

There are, however, workarounds, which are documented at:
http://backuppc.wiki.sourceforge.net/change+archive+directory

-- 
Backuppc no compression when change topdir
https://bugs.launchpad.net/bugs/246659
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