You can run into a lot of issues when you re-version something. BizTalk uses a lot of hard references.
But for you specific problem, did you check to see if maybe it got deployed into another Application? Maybe the default Application?
Also, make sure if you have a Solution with many projects in it and you are deploying from Visual Studios that you do a full deployment of the whole solution and not just the Orchestrations. Or the will do just what you said and disappear.