@SajidRavat There has been a new release of PSF (version 1.0.231110.2) with a way to support Deletion Markers for registries which allows hiding of specific registry keys or registry values in the virtual environment.
You can use MSIX Packaging Tool to apply this fixup providing regex strings for Registry Keys and Values.
Please try using that and let us know if that works for you.
You can also share you MSIX package and Java use case for us to look into this.
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