Okay, so I actually had a 5th node which I couldn't remove. It was also unused, but apparently had a neighbour still configured (the neighbor node 61 is an active device). Once I managed to remove that neighbor, I could remove the node.
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Z-Wave Syncing - started for "124 - Relay Power Switch"
Z-Wave Syncing - retrieved module neighbors list: 61
Z-Wave Syncing - assigning return route to "124 - Relay Power Switch"
10 Nov 2018 at 13:41:05
Z-Wave Error Syncing - failed
Z-Wave Error Timeout waiting for "124 - Relay Power Switch". Module might be asleep, or is unreachable.
10 Nov 2018 at 13:41:23
Z-Wave Error failed to remove module 128 from controller (read failed: [Errno 6] Device not configured)
Z-Wave Error serial port communication error: read failed: [Errno 6] Device not configured
Z-Wave Error Z-Wave 3.95 static controller might be disconnected
Z-Wave Error silently retrying serial connection every 5.0 seconds
Interface Failure lost connection with interface
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Z-Wave Optimizing - started network optimization for nodes: 61
Z-Wave Optimizing - starting "061 - Allrum Keyboard"
Z-Wave Optimizing - ping completed in 36 ms
Z-Wave Optimizing - finding neighbors
Z-Wave Optimizing - requesting neighbor list update
Z-Wave Optimizing - neighbor list updated from 66, 67, 71, 73, 81, 82, 94, 96, 124, 131 to 20, 65, 67, 69, 71, 73, 74, 75, 81, 82, 94, 96, 97, 103, 134, 135, 139, 143, 147, 151, 152, 155, 158, 159, 160
Z-Wave Optimizing - finished "061 - Allrum Keyboard"
Z-Wave Optimizing - complete
Z-Wave Optimizing - update succeeded: "061 - Allrum Keyboard"
Z-Wave Syncing - started for "124 - Relay Power Switch"
Z-Wave Syncing - retrieved module neighbors list: - none -
Z-Wave Syncing - assigning return route to "124 - Relay Power Switch"
Z-Wave Error Syncing - failed to assign return route
Z-Wave Error Syncing - failed
Z-Wave Error No response from "124 - Relay Power Switch". Module might be asleep, or is unreachable.
Z-Wave removing from controller failed module "124 - Relay Power Switch"
Z-Wave reloading module information from controller
The four nodes left to remove have eachother as neighbors, so I can't optimize them to get rid of the neighbour statements.
My nodes which I can't remove are:
072 with neighbor 116 and vice versa
086 with neigbor 107 and vice versa
Deleting the neigbor records for the nodes should solve my problem.