Hello there,
In general, Sysprep does not remove applications. Some applications are sensitive to sysprep, but those are rare exceptions. Sysprep strips out the machine-specific settings like activation ID and SID, while leaving the installed programs for ease of deployment.
Sysprep has an additional provider that's added in Windows 10 and Windows 8 to clean Appx packages and to generalize the image. The provider works only if the Appx package is a per-user package or an all-user provisioned package.
To resolve this issue, remove the package for the user who's running sysprep, and also remove the provisioning.
I hope this information helps. If you have any questions please let me know and I will be glad to help you out.
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