>>>1. will this property work on message level or payload level?
Message level
>>>2. my target system is same but I will be using different type of adapter (File and IDoc_AAE) will the sequencing still work ?
it doesn't matter, it should still work.
>>>3. if I am going to use two separate target system will this also work in the same way? (just curious .. not fit to my scenario)
You can't guarantee the sequence when you have two different receiver systems. if a message fails for a receiver system it doesn't stop the flow for other receiver.
