How to Disable the Per-User MSI Warning
Use the following procedure to disable the dialog box that warns about per-user MSI issues. For more information about this setting, see the Advanced element in Settings Dialog Box.
To disable the per-user MSI warning
Right-click any tree node item, and then click Settings in the Updates Publisher console to open the Settings dialog box.
Click the Advanced tab, and then enable Do not display warnings about per-user MSIs.
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Reference
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Best Practices for Updates Publisher