I’m working through a known BizTalk issue that requires you to remove your application from BizTalk to be able to use VS2005 to deploy and ran across some helpful command-line stuff until a more permanent fix is applied:
To stop/start the applications there is a sample app that ships with BT:
<BizTalk Install Dir>\SDK\Samples\Admin\ExplorerOM\ApplicationManager
Use the BTSTask command to remove an application:
btstask removeApp /ApplicationName:<app name>
and Import bindings:
BTSTask ImportBindings /Source:"%BindLoc%" /ApplicationName:<app name>