I tried using App4RPG it a couple times for projects and each time got weird lockups or failures.
I share my experience with it (and I used only it for small quick transactions, not bulk ETL style...) , one should isolate IMHO the code using *ARDPGM in its own program and being very disciplined in command handling transactions/commit statements and disconnects.
I noticed for example that it really didn't like commands like RCLACTGRP (that were issued in my local architecture at the end of the job before logoff... so i bypassed it).
Being internally App4RPG dataqueue based internally you can in any case reduce the read on dtaq timeout to limit the lockup time in such weird conditions. Also is open and debuggable.
App4 implements *ARDPGM, i.e. you can query a mysql with STRSQL and interactive tools etc. .... Scott's are just direct method calls to JDBC. Different beasts and tools for different requirements and context.
In any case for any "big intergration work" involving hundreds of tables plus fields to sync, I would use a proper ETL tool to move data around. Talend Open (before Qlik "demolition" of the Open product) was pretty nice to use because basically produced a jar + sh file from the visual flow IDE ... and being java could schedule it on everything... i.e. directly on the IBMi or invoke it when needed from ILE.
Never used node-red, it is included in the ibmi repos..... I don't know the status/level of the GUI for heavy DBMS usage, maybe someone will share
https://developer.ibm.com/articles/implementing-etl-flows-with-node-red/
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