I would first apply a more current fixpack to your 11.0.0.3. To my knowledge,v11 is still supported. 11.0.0.26 is current the last I looked. IBM App Connect Enterprise v11.0 - Fix Pack 11.0.0.26 They probably do not want to support v11.0.0.3 because they would not be able to provide you a fix at that level.
Then I would follow the v12 doc which is pretty good. Migrating - IBM Documentation
Doing the in-place migration has worked out well for us and it allows you to go back and forth between v11 and v12 if that is needed.
I hope this helps.
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Robert Rehms
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