Why don't you just make a copy of the config file(s) and let apt
proceed normally and then restore the old config files after the
backup.
Then if anything breaks when you run with the old configs you can fix
it based on the error messages.
But based on my recollection, most of the changes were additions of
new variables or minor grammar/typo corrections, so it may just work
as-is.

What I did was to do a 'diff -ruw' between my edited 3.1.0 config file
and the original virgin 3.1.0 config file.
Then I applied that as a *patch* to the new 3.2.0 config file. I did
this across versions (3.1.0 --> 3.2.0) and across Distros/architecture
(Fedora 12/X86 --> Debian Lenny/armel). I think of several dozen
config changes only 2 hunks failed to patch and it was pretty obvious
how to fix them.

Boniforti Flavio wrote at about 15:18:40 +0100 on Monday, February 7, 2011:
 > Hello again.
 > 
 > > I'm in the middle of upgrading on my Debian Sid of BackupPC 
 > > and get many differences in the config.pl file. Besides the 
 > > differences depending on custom parameters (done by me), the 
 > > main differences I see are like:
 > > 
 > > -$Conf{BackupPCNightlyPeriod} = '1';
 > > +$Conf{BackupPCNightlyPeriod} = 1;
 > 
 > OK, not having too much time, I decided to go for the simple solution: I
 > told APT to maintain the actual config.pl
 > 
 > What now happened is that the upgrade *failed*, but still the 3.1.0 is
 > running.
 > 
 > Here the excerpts I got from APT:
 > 
 > Starting backuppc...2011-02-07 14:16:05 Another BackupPC is running (pid
 > 1110); quitting...
 > invoke-rc.d: initscript backuppc, action "start" failed.
 > dpkg: error processing backuppc (--configure):
 >  subprocess installed post-installation script returned error exit
 > status 1
 > 
 > [...]
 > 
 > Errors were encountered while processing:
 >  backuppc
 > E: Sub-process /usr/bin/dpkg returned an error code (1)
 > 
 > Where may I look for errors?
 > 
 > Thanks,
 > Flavio Boniforti
 > 
 > PIRAMIDE INFORMATICA SAGL
 > Via Ballerini 21
 > 6600 Locarno
 > Switzerland
 > Phone: +41 91 751 68 81
 > Fax: +41 91 751 69 14
 > URL: http://www.piramide.ch
 > E-mail: flavio AT piramide DOT ch 
 > 
 > ------------------------------------------------------------------------------
 > The modern datacenter depends on network connectivity to access resources
 > and provide services. The best practices for maximizing a physical server's
 > connectivity to a physical network are well understood - see how these
 > rules translate into the virtual world? 
 > http://p.sf.net/sfu/oracle-sfdevnlfb
 > _______________________________________________
 > BackupPC-users mailing list
 > BackupPC-users AT lists.sourceforge DOT net
 > List:    https://lists.sourceforge.net/lists/listinfo/backuppc-users
 > Wiki:    http://backuppc.wiki.sourceforge.net
 > Project: http://backuppc.sourceforge.net/

------------------------------------------------------------------------------
The modern datacenter depends on network connectivity to access resources
and provide services. The best practices for maximizing a physical server's
connectivity to a physical network are well understood - see how these
rules translate into the virtual world? 
http://p.sf.net/sfu/oracle-sfdevnlfb
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List:    https://lists.sourceforge.net/lists/listinfo/backuppc-users
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