Yes and no. If a client checks in while the service is down, the client should see the JSS as unavailable. No harm, no fowl. The client will check back in and I'd think by then your service would be up.

I could see an issue if you bounced the service while policies were actively being run. Long long ago, I requested a "maintenance mode" that would refuse client connections so that you could then bounce the service safely. However, that was long before The Nation and the formal feature request function so I think I'll repost that request now.

Posted: https://jamfnation.jamfsoftware.com/featureRequest.html?id=843