This issue has been fixed with Open Transport 1.1.1. If you are not using Open Transport 1.1.1 with ARA, you should update Open Transport. Open Transport 1.1.1 is available on Apple computer's online Software Update locations. Open Transport 1.1.1 is only supported as an update with Open Transport 1.1. Open Transport 1.1.1 is supported on System 7.1.x and System 7.5.3 and later.
NOTE: This issue is independent of whether you are using ARA 2.0.1 or 2.1.
Below is a description of tests which illustrate this Open Transport 1.0.7 and ARA 2.0.1 issue:
Let's say you have zone A and B that are local. The ARA client is in zone A. The ARA server is on a different internetwork in zone C. In addition, let's assume that you can't place the client in zone B via the AppleTalk control panel.
Test 1
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If the client is connected to zone A with LocalTalk, then you lose all devices in both zone A and B. All devices in zone C are available (as well as devices in other remote zones). This confirms what you reported in your escalation.
Test 2
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If the client is connected to zone A with Ethernet, then devices in zone A and the remote zone C are available, but devices in zone B are not.