Hi Melih,
Could you let your partner callback process engine after they complete their job? You could send the executionId as a parameter including the async request message. And the partner should know how to callback the process after their job. Then we could put the timer in a transition, and timeout will signal the specified transition and let execution go on running.
If the partner cannot callback process engine, then we could use a decisionActivity to verify whether the partner has done their job, yes will continue, no will go back to the stateactivity.
But be careful when you chose the second way, because there is bug for this scenario, please refer https://jira.jboss.org/browse/JBPM-2794. This bug has been fixed in the jBPM 4.4.
In my opinion, I think it is definitely a bug that process won't delete related timer after it was signaled by external system and we should find a way to handle it.