@delputnam Apologies for the delay - I had to have a chat with Andrew about this as it's an unusual issue.
If you restored the second Mac from the first, including all of your Application Support folder, it's possible that the server UID for each Mac is the same, resulting in Alfred thinking both Macs are the same device.
Here's how you can resolve this:
Delete all devices from Alfred Remote
Quit Alfred on both Macs
Navigate in your user directory to ~/Library/Application Support/Alfred 3/ and delete the /Remote/ folder completely on both Macs
Restart Alfred and re-connect your devices - each one should now be given its own server UID
Let me know how you get on
