I'd also go for a database solution. If DBD::DB2 contains (unfixable?) bugs, you might want to go for another database driver. I'm not MySQLs biggest fan, but for this task, synchronization, it looks like it can provide an adequate solution. Of course, the ideal solution would be if you can fix the bugs in DBD::DB2. ;-)
Of course, many other solutions are possible, either written from scratch, or piggybacking on something else (email for instance).
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