So it looks like something broke in the most recent update to the hue connect smart app. I had multiple bridges working but after the update only one bridge will work. It appears that the bulbs that are getting added to the bridge are being hijacked by another bridge. When you go to add new bulbs to a bridge that they are paired to via hue app the add bulbs page in the smart things app is showing a mismatch of bulbs. IE some bulbs from both bridges are appearing in a list of bulbs. I looked through the code a bit for the connect app and it appears that the bridges are getting confused by the smart things hub and it is polling to build the list from one bridge, then switching to the second bridge when it goes to discover bulbs and back and forth. This is then setting the bulbs to attach to the wrong bridge when you add them and those they are no longer able to receive commands because the wrong hue bridge is getting asked to turn them on or off. it appears that the scone bridge added is always be set as the main bridge or the bridge that the smart things app is looking to talk to.
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I’m having the same problem.
I keep my lights separate from the kids hue lights so that they can control theirs without changing mine. The two hubs are getting confused in SmartThings.