If I am understanding the case correctly, the desired functionality can be implemented by adding the following script as noted in this MultiSelect DataSource manual filtering demo:
<!-- IMPORTANT: Update filter state of the widget -->
Please check the edited versions of the Dojo you've sent me:
In both of the above demos, after adding the above code line, the filtered items are being correctly selected and after the initial selection, we can continue selecting/deselecting all MultiSelect items.
Please check the linked Dojo projects and let me know if they demonstrate the functionality you want to acheive.
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