Killing an application should always be the very last course of action, you should always build in a clean close/exit in the same way that manual users do. For some applications or interfaces killing an application can cause locking or api issues. It sounds like your application has this issue, probably killing the app is impacting the Hllapi interface that Blue Prism is trying to use - I suggest building a clean exit routing/object that keeps pressing whatever the exit keys are for that mainframe (usually a mixture of F3s and/or F12s in my experience - but could be anything, ask an SME), and cleanly exit.
