The fact that CM servers have a 1024 limit on ARP table entries is a well-known issue. I found the following blurb in several of the administration guides, though:
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Do not install Cisco Unified Communications Manager in a large Class A or Class B subnet that contains a large number of devices. When you install Cisco Unified Communications Manager in a large subnet with a large number devices in that subnet, the Address Resolution Protocol (ARP) table can fill up quickly (maximum 1024 entries, by default). When the ARP table gets full, Cisco Unified Communications Manager can have difficulty talking to endpoints and cannot add more phones.
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I know that subnets this large would not be a recommended design, but the "by default" suggests that you could reconfigure this limit on CM, at least for the short-term until the logical topology could be re-designed/deployed. I haven't found any supporting documentation on how to do this, if it's even possible.
Thank you!