The two models you've provided here are not valid EMF models (right-click their root > validate). Specifically, the "observers" Object contain actions that have a "by" reference that is set to be of type "ifconf:Pid"... but point towards "ifconf:Instance" Objects. (Either that or your metamodel is not valid and "Action.by" should not be of "Pid" type. You should have exceptions logged in your error log when you try and compare these models.
As these models are now, we cannot reproduce the issue from our side.
Thanks for your help, you're right !
I have just deleted the problematic elements (I will solve this pb later) and know I'm able to compare them.
But when I store the results as .emfdiff file it is 4 times bigger than my models (the models are nearly 400 bytes and the emfdiff is 1.5 M bytes) ! is there a way to store only the elements that doesn't match ?
No, with EMF Compare 1, the comparison stores all referenced objects from all two/three models and cannot be trimmed. This is something which we aim at enhancing with the ongoing development of EMF Compare 2.