I have an environment that - if I understand your plans right - more or 
less corresponds to what you intend to do and that has worked without 
problems for me during a couple of years:
  - Several independant bootable partitions, each with its own copy of
    backuppc code, of /etc/backuppc/config.pl and of /var/lib/backuppc
    (in fact, the /etc.backuppc/config.pl files are copies of a
    "standard" template)
  - another file system (in fact another disk) that contains
      (a) the backup data,
      (b) the local data needed by backuppc - i.e. the "hosts" file
          with the client list, and the "pc" directory with the
          profiles of each host, but also
      (c) the password file used by lighttpd - my httpd server.
    (b) and (c) could be anywhere, having a single copy of these data
    makes maintenance easy and avoids accidently introducing conflicting
    configuration data. The /etc/backuppc/hosts and .../pc nodes of each
    OS partition are soft links to the effective data.

Evidently, I am careful not to reboot while backuppc is running.

Normally, my OS partition are different versions of my preferred OS - 
initially Mandriva, at present Mageia (a production version and several 
versions with software under test).

While I evaluated potential candidates for the succession of Mandriva, I 
had different Linux platforms on different partitions, and positively 
evaluated that backuppc also worked in such a multi-platform 
environment, and that the single copy of the backup data was not 
corrupted. I am sure that this worked between Mandriva and Fedora, 
between Mandriva and Mageia - I had tested other platforms, but for some 
of them I had given up the evalutation early in the game, not sure in 
which combinations I had gone as far as testing backuppc coexistance.

Unless the representation of the data saved by backuppc is modified and 
unless the format of the host list and the host profiles is modified, 
this coexistance should also work if different versions of backuppc run 
on different partitions - but I have not explicitely tested this (except 
the evident test that happens when a new version of backuppc is installed).

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