Perhaps you should try to print out whats going on?

print qq($prefix1/n$prefix2/n);

print qq($sep1/n$sep2/n);

for my $folder ($imap->folders) {
        print qq(Folders: $folder\n);
        $imap->select($folder) or warn "Error: $imap->LastError\n";
        $folder =~ s/^$prefix1/$prefix2/g;
        print qq(First substition: $folder\n);
        $folder =~ s/$sep1/$sep2/g;
        print qq(Second substition: $folder\n);
        $imap->migrate( $imap2, "ALL", $folder ) or warn "Error: $imap
+->LastError\n";
}
[download]

Regards, Karl