I have done File to IDOC scenario and tested it end to end successfully. For same have done all require configuration setting in R/3 like defining logical System and partner profile. And it sends new IDOC successfully in R/3 with status code 50 (IDoc added).
But when I create new logical system and partner profile in R/3 and when I use same logical system in my above mention scenario then my new generate IDOC in R/3 return status code 56 (EDI: Partner profile inbound not available). But same scenario work fine with my earlier partner profile. Here I have done all require changes at adapter level like adapter specific identification and same new logical system I have update in SLD with my business system Logical System Name.