Tested versions
v4.6.dev4.official [bd2ca13]
System information
Godot v4.6.dev4 - Windows 10 (build 19045) - Multi-window, 1 monitor - Vulkan (Forward+) - dedicated AMD Radeon RX 6600 (Advanced Micro Devices, Inc.; 32.0.21001.9024) - AMD Ryzen 5 5500 (12 threads) - 15.87 GiB memory
Issue description
When Resources are linked, it displays an icon near the property telling you how many Nodes are actually using these, For normal Resources, when using the 'Revert Value' button, it decrements the counter and displays accordingly. For custom Resources, though, it still shows the previous amount:

Funnily enough, using Clear or Revert Value in the property dropdown does not cause the issue.
Steps to reproduce
- Create a custom resource in the Inspector from a Node
- Duplicate this Node
- It will show up the link icon, indicating there's 2 Nodes using the same Resource
- use the 'Revert Value' button
- Check the duplicate and see how the link still shows up with the wrong amount.
Minimal reproduction project (MRP)
default-issue.zip