This feels like a shot in the dark but...
Should a single Native Messaging host be able to communicate with the same extension installed on multiple chrome profiles?
I'm working on an extension which is installed to both my personal and work profiles. But it seems that the Native Messaging host only sends messages to the most recently connected instance of the extension.
I don't believe this is addressed in the Native Messaging documentation and I've run out of search ideas, thanks in advance for any help!
When nativeMessaging API is used it starts an instance of native app each time a connection is created by the extension so such an instance can communicate with its "parent" extension only. Consequently, there should be no problem.
In case you want to use chrome.runtime.onConnectNative to do the reverse (to connect from a native app to an extension which will work even when Chrome is closed) see crbug.com/967262 for more info or create a new issue there asking for details. Judging by the bits I see this feature is available only on ChromeOS and it's even disabled by default.