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L2 and L3 connect now stops working

I have a reoccurring problem. Our environment is primarily Juniper EX series. Maps have been built and working great but if a switch goes down due to power or reboot for maintenance I lose the link that were automatically found. They turn red. I try reconnecting them in orion but I get 0 connections. This also happens with our aerohive access points when they reboot for whatever reason. 

Very frustrating and support has never been able to resolve it. I make sure all the resources are monitored on each side. Within the nodes I can see that SW knows the connections but can't get them back on the map. 

Any help will be appreciated.