email me and I will try to help you through this.
However, you need to use a proc called hcix12splitinterchange (anyway the name is close to that if not exact). on the Inbound thread Inbound Tps.
What that does is to split off the X12 ‘envelope’ and place the data in each messages metadata.
If you say each file has ISA GS ST 835 SE GE and IAE then you would want to give the split interchange proc an argument of GS so that it gives you from the ST through the SE for each message.
Then assuming the 835s aree to come out X12, you need to place a proc called hcix12buildinterchange (or a similar name) in the Outbound Thread Outbound TPS. This proc adds the saved off envelope information onto each ST through SE.
If you have a batch file such that there are more than one set of ST through SE 835s per file you will need to set IDE Batch X12 configuration (I believe that is on the Inbound and Outbound Tabs of the respective threads).
Hopefully you are well versed in ITERATES as X12 is a lot of repetitions.
If you still would like to chat off line email me and I will try to help.
email: jim.kosloskey@jim-kosloskey.com 29+ years Cloverleaf, 59 years IT - old fart.