There’s no logical reason why the Harmony integration should affect Zwave at all. It’s not the same protocol.
That said, it doesn’t mean that there isn’t something in the SmartThings architecture that is causing your local network to get out of sync with your cloud account when you do the harmony integration, Or something like that. People have been reporting that a bunch of zigbee devices will go out, or a bunch of Z wave devices will go out, when they shouldn’t. Nothing to do with harmony, just you change one thing, and suddenly you lose half of one of your local networks.
And forcing a resynch with the cloud account by taking the hub off-line for about 15 minutes often seems to fix it, even in situations when it shouldn’t.
So I do suspect some synchronization issue between the cloud and the hub but who knows?
I’m glad you got something working. 