Hi Papi,
The ABAP adapters like the IDOC and HTTP needs extra effort to do the migration as William Li said in this document http://a248.g.akamai.net/n/248/420835/22d6349e94e403fe11634db52ad14a44617cfbf79656ebed6d7a50c13888b670/sapasset.download… as they didn't need sender agreements because they belonged to the ABAP stack.
Check this note 1826572 - Migration Tool for Integration Directory Objects - updatesthe problem seems to be corrected since 7.30 SP11, 7.31 SP09 and 7.40 SP04.
Regards.