Hello,
Welcome to Microsoft Q&A!
After confirming with the team, I have some things to share.
First of all, the platform does attempts to remove the C:\ProgramData\Packages{appName}<userSid>\SystemAppData folder at package uninstall, but like other file system locations, the remove is best-effort basis, i.e., even if we hit an error we don’t want to fail the uninstall. So you should only have an empty C:\ProgramData\Packages{appName}<userSid> folder left after uninstall.
Cleanup of this per-user folder happens when the current user is being removed. It is safe to manually delete the empty per-user folder, if desired, but it requires admin privilege.
If the existence of an empty and harmless folder is not causing any issue, then there should be no problem.
Thank you.
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