I now have everything working with out doing a reset. ST now sees both Harmony Hubs (Family Room & Theater Room).
What I happen to find was when I was logged into my SmartThings account (https://graph.api.smartthings.com) under My Devices and looking at my Harmony Hub, it showed all the devices I checked off to allow the Harmony Hub to control through ST when I first set it up on the Logitech’s Harmony setup page. But I was not able to see any of that on ST app, so that is why I kept getting all the warning about not able to remove the HH.
So what I did was setup my Harmony Hub on Logitech website again and added ST as a device, but did NOT add any devices (lights, switches, activities) for the HH to control through ST, if there was a device that had a check mark next to it I removed it.
Now all this time I still have the Harmony Hub showing that it’s still there and Active, even thou it was physically removed from my setup. So now I went back to Marketplace again on the ST app and added the Harmony Hub and after a few seconds it recognized the HH again. I did not add the HH to anything just yet, what I did was go back and logged into my SmartThings account and now noticed the HH in My Devices has no devices actives associated with it.
So I went to my older 3 activities that I renamed “XxxNOT-USED-01xxX”, etc… and was able to remove them with out a problem this time. After I was finished remove anything related to the HH I went in and removed the Harmony Hub. Once the HH was remove so was the link with Harmony account & ST account.
Now with both Harmony Hubs (Family Room & Theater Room) set up for each room I added ST back, but for right now I did not add any devices the the Harmony to control via ST. I went back into Marketplace and added the HH, I now was requested to sign into my Logiteh account to link ST to it. Once I clicked done in a few second it showed it found my two Harmony Hubs and the 6 activities I created for them.
I was also about to connect the two Harmony Hubs activities (Theater Room - Watch-TV, Family Room- Watch-TV, etc…) To our Amazon Echo.
I hope this might help anyone who might have the same issue that I had. Hey @scottalex
Thanks again fo everyone who responded!