"java.project.resourceFilters" not honored when setting up new project

I'm getting errors like below while opening java projects. I've tried cleaning workspace, but it just happens again when I re-import.

Java Model Exception: Error in Java Model (code 1006): _/src/xx/xx/xx/xx/protectedModel/view/client/.ade_path [in protectedModel_48d582b1] is not on its project's build path
	at org.eclipse.jdt.internal.core.JavaElement.newJavaModelException(JavaElement.java:584)
	at org.eclipse.jdt.internal.core.Openable.generateInfos(Openable.java:254)
	at org.eclipse.jdt.internal.core.Openable.openAncestors(Openable.java:528)
	at org.eclipse.jdt.internal.core.Openable.generateInfos(Openable.java:248)
	at org.eclipse.jdt.internal.core.Openable.openAncestors(Openable.java:528)

That .ade_path has a symlink that points to a different file on a different filesystem and the error is legitimate.
But the problem is that I already have set the below filters:

"java.project.resourceFilters": [
        "node_modules",
        "\\.git",
        "\\.ade_path"
 ]

I've some projects which are working fine, I'm not sure how.
If I dig up their .project I can see below snippet is already added. But same filter is missing for .project files corresponding to non-working project setups.

       <filteredResources>
		<filter>
			<id>1675774599078</id>
			<name></name>
			<type>30</type>
			<matcher>
				<id>org.eclipse.core.resources.regexFilterMatcher</id>
				<arguments>node_modules|\.git|\.ade_path|__CREATED_BY_JAVA_LANGUAGE_SERVER__</arguments>
			</matcher>
		</filter>
	</filteredResources>

Start by tracing how the Java extension creates or updates the generated .project file when a new project is set up, using java.project.resourceFilters as the behavior to follow. Reproduce with a project containing .ade_path and compare working and non-working .project files; done means the configured filters are present and the error no longer appears.