Oops - I see a bug in BackupPC_refCountUpdate when it tallies up all the reference counts for each backup. It doesn't include the hybrid (migrated) backups.
Here's the diff I just pushed to git.
diff --git a/bin/BackupPC_refCountUpdate b/bin/BackupPC_refCountUpdate
index 0c2e027..aa1f9f9 100755
--- a/bin/BackupPC_refCountUpdate
+++ b/bin/BackupPC_refCountUpdate
@@ -410,7 +410,7 @@ sub updateHostRefCounts
my $poolCntFileNew = sprintf("%s/poolCntNew.%d.%02x",
$refCntDestDir, $compress, $refCntFile * 2);
for ( my $i = 0 ; $i < @Backups ; $i++ ) {
- next if ( $Backups[$i]{version} eq "" || $Backups[$i]{version} =~ /^[23]\./ ); # skip pre-V4
+ next if ( $Backups[$i]{version} eq "" || ($Backups[$i]{version} =~ /^[23]\./ && !-d $bkupRefCntDir) );
my $bkupNum = $Backups[$i]{num};
my $refCntBkupDir = "$TopDir/pc/$host/$bkupNum/refCnt";
my $poolCntHostFile = sprintf("%s/poolCnt.%d.%02x", $refCntBkupDir, $compress, $refCntFile * 2);