Sorry for the inconvenience caused.
We have followed the steps as you provided in your first update. But we were unable to reproduce the issue in that case. Please check the image
But while following the below steps we can able to reproduce the issue which is reported by you
1. 1. After unchecking the New South Wales, Victoria, south Australia and western Australia, we again type acre in search box.
2. 2. Now acre with its corresponding parent Nodes get checked
3. 3. After clearing the filter, we found that all the nodes under Australia get checked.
We overcome this issue by maintaining the indeterminate nodes in separate array and make it check only when it is changed by user interaction.
Note: You can disable the autoCheck property to achieve the independent checked state of parent and child Nodes
Please check the sample and get back to us if we misunderstood your query or need any further assistance.