Wix Bundle (per user) Upgrade uninstalls a per machine MSI

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Wix Bundle (per user) Upgrade uninstalls a per machine MSI

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I am running into a problem with the upgrade of my Bundle installer. I'm trying to do a major upgrade where 2 other MSIs have been upgraded. These are per user MSIs. Some other MSIs have been unchanged.

Most of the upgrade works successfully. However, one of my unchanged MSIs (usb_support_installer for reference) gets uninstalled. This MSI happens to be a per-machine MSI. I see the following in my log files:

in my logs
"[20C8:200C][2016-09-28T15:54:06]i000:  PlanPackageBegin
[20C8:200C][2016-09-28T15:54:06]i000:   PackageId = usb_support_installer
[20C8:200C][2016-09-28T15:54:06]i000:   State = Present
[20C8:200C][2016-09-28T15:54:06]w322: Skipping cross-scope dependency registration on package: usb_support_installer, bundle scope: PerUser, package scope: PerMachine
[20C8:200C][2016-09-28T15:54:06]i000:  PlanPackageComplete"

and then further down in the logs
[20C8:200C][2016-09-28T15:54:06]i201: Planned package: *usb_support_installer*, state: Present, default requested: Present, ba requested: Present, execute: None, rollback: None, cache: No, uncache: No, dependency: *None*

This seems to suggest that my "usb_support_installer" package is not considered a dependency and gets uninstalled once the previous Bundle version is uninstalled.

Sure enough, I see this in my logs for the uninstall of the previous Bundle version
[1D4C:15A0][2016-09-28T16:45:25]i301: Applying execute package: usb_support_installer, action: Uninstall, path: (null), arguments: ' ARPSYSTEMCOMPONENT="1" MSIFASTINSTALL="7"'

Wondering if Burn supports per user Bundle scope with some per machine scope packages? Wondering if I need to do something additional to handle upgrades of such bundles/packages?

Appreciate any help