AppV5 - Package failed configuration in folder with error 0xA040132A-0x3

When publishing AppV5 applications on a PVS server we sometimes encounter an issue where packages do not load.  There are usually events logged to event viewer with the following:

Package {5075e8a4-4335-4101-991e-be88f5862575} version {940e4d49-af37-428c-a129-3bd37e3e4539} failed configuration in folder 'D:\AppVData\PackageInstallationRoot\5075E8A4-4335-4101-991E-BE88F5862575\940E4D49-AF37-428C-A129-3BD37E3E4539' with error 0xA040132A-0x3.

With another event that follows:

Part or all packages publish failed.
 published: 14
 failed: 10
Please check the error events of 'Configure/Publish Package' before this message for the details of the failure.


This issue is typically caused by two factors: folders not existing in the "PackageInstallationRoot", in my example that is D:\AppVData\PackageInstallationRoot.  You can find this value in the registry here:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\AppV\Client\Streaming /v PackageInstallationRoot /d D:\AppVData\PackageInstallationRoot

and registry entries existing here:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\AppV\Client\Streaming\Packages

There are more values in the registry then the folder above.

What you will find is a mismatch between the number of keys in Packages and the number of folders in your PackageInstallationRoot path.  For us, our error was we had 14 folders existing in that path, but 10 of them were missing.  But we had all 24 values existing in the registry.

To fix this error I created a script to create the missing folders that were found in the registry and doing a get-appvpublishingserver | sync-appvpublishingserver

D:
cd D:\AppVData\PackageInstallationRoot
for /f "tokens=1-6" %%a IN ('reg query HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\AppV\Client\Streaming\Packages /s ^| findstr /i /c:"PackageRoot"') DO mkdir %%c

And then all applications were able to be published without issue.