ephDev,
is this a regular task or a once off?
You can build a custom procedure to make your queries on DB2 and MySQL and call this procedure from nuBuilder with runIt() function.
ephDev,
nuBuilder version 2 work only with MySQL database, so if you want to manage DB2 records you must create a copy, or replication, in MySQL.
This could be done:
creating a custom PHP procedure to copy every x time changed records from DB2 to MySQL (as I described in my previous post);
using IBM Datapropagator to replicate DB2 to MySQL (have a look at this thread).
NuBuilder version 3 will allow to connect with DBs other than MySQL, using PDO.