Get-AppvClientPackage : Application Virtualization Service failed to
complete requested operation. Operation attempted: Get Packages. Windows Error:
0x800703E7 - Error performing inpage operation Error module: Manifest Library.
Internal error detail: 43E01234800703E7. Please consult AppV Client Event Log
for more details.

Checking in the registry in path "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\AppV\Client\Packages", it lists the successfully published applications by App-V GUID. The successfully published appear to function. The successfully published applications appear to function with exception to the applications with a corrupted Manifest.xml.

Once delivery of App-V packages fails due to the corrupted Manifest.xml, it will cause other 0x87D01290 errors to occur. This is due to the App-V client hanging and not responding to the ConfigMgr agent, when it querying for published App-V applications. At this point, new App-V applications will not be deployed/published to the computer, as the agent is unable to determine what is and isn't published.

This error 0x87d01290, effects App-V User and Machine targeted applications. 

Please note that the 0x87D01290 error is a symptom of a issue, but not the root cause of the issue itself.  

Discovery

1. Home > YourSCCMReportingServer_URL > Software Distribution - Application Monitoring > Application Compliance.
   
2. Select your application in the drop down menu and then collection (All Windows 10 clients for example). Hit "View Report".
   
3. Once the report loads, click on the Application link, this will allow you to dig into the results for more details. Once loaded again, click on the number of errors link, this will show you a breakdown of the errors. You should see an Enforcement State error "An error occurred when querying the App-V WMI provider", this is the 0x87d01290.
   

Component: AppVHandler
Note 0x87d01290 error.

AppVPackageQueryClient5X::GetPackageDataByPackageGUID() failed for
virtual application [XXXXXXXXXXXXXX]. (0x87d01290)

Log: C:\Windows\CCM\Logs\AppIntentEval.log

Component: AppIntentEval
Note Current State = Error due to App-V being unable to do the evaluation.

ScopeId_XXXXXXXXXXXXXX/RequiredApplication_XXXXXXXXXXXXXX/8 :- Current
State = Error, Applicability = Unknown, ResolvedState = None, ConfigureState =
NotNeeded, Title = ApplicationIntentPolicy

Found better solution to discover all the 0x87d01290 errors. In SCCM, create a query with the WQL below to list all devices with this error, and the applications that is currently blocked from delivery. This is a dynamic query, so computers will fall out of the collection as they are fixed. Please note the query will list User and Computers with 0x87d01290 errors.

All applications that are not being delivered due to error.

select 
	SMS_R_System.Name,
	SMS_R_System.ResourceId,
	SMS_R_System.OperatingSystemNameandVersion,
	SMS_AppDeploymentAssetDetails.AppName,
	SMS_AppDeploymentAssetDetails.StatusType,
	SMS_AppDeploymentAssetDetails.EnforcementState,
	SMS_AppDeploymentAssetDetails.CollectionName,
	SMS_AppDeploymentAssetDetails.Technology 
from 
	SMS_R_System inner join SMS_AppDeploymentAssetDetails 
on 
	SMS_AppDeploymentAssetDetails.MachineID = SMS_R_System.ResourceId 
where 
	SMS_AppDeploymentAssetDetails.StatusType = "5" And 
	SMS_AppDeploymentAssetDetails.Technology = "AppV5X" And 
	SMS_R_System.OperatingSystemNameandVersion = "Microsoft Windows NT Workstation 10.0" And 
	SMS_AppDeploymentAssetDetails.EnforcementState = "5001"

Get-AppvClientPackage : Application Virtualization Service failed to
complete requested operation. Operation attempted: Get Packages. Windows Error:
0x80070005 - Access is denied Error module: Manifest Library. Internal error
detail: 43E0123480070005.

On 3 instances of checking 17 machines, we have found that the Manifest.xml has been OK, but the App-V error still appears when running the Get-AppvClientPackage cmdlet. We think this could be due to malformed XML’s in the user targeted space? This is speculation, yet to look into and confirm. Looked into the user space with malformed XML's and found no issues, used a PowerShell script to recursively check all the App-V XML's  in the user space (AppxManifest.xml, FilesystemMetadata.xml, PackageHistory.xml, StreamMap.xm, DynamicConfiguration.xml and UserManifest.xml) but found no issues. 

So far we have only found this issue in Manifest.xml’s.

1. Not sure when corruption occurs, on delivery of files?
2. ConfigMgr AppDiscovery is run, an application is missing, triggers action to publish missing application.
   
3. App-V attempts to publish the application, it breaks at this point(?). 
4. ConfigMgr agent uses some WMI calls (App-V cmdlets) to query what applications are on the computer, WMI is now broken due to the attempt to publish previously.
5. Broken WMI (App-V cmdlets) cause ConfigMgr to report an evaluation error, because it can not query correctly/anymore.
   Which each ConfigMgr query for application thereafter, it will report a 0x87d01290.

mofcomp "C:\Windows\WinSxS\wow64_microsoft-windows-a..appvprogrammability_31bf3856ad364e35_10.0.17134.1_none_dbe491204bf36f48\Microsoft.AppV.AppVClientWmi.mof"

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\AppV\Client\Packages

Update 3 09/29 = I lied in update 2, seems only work on some machines and is not reliable. 
Update 2 09/28 = Confirmed fix/hack works (hurrah).

Update 1 09/28 = Testing in progress, seems to work.

Credits

Mal Lagden for provding the other half of the solution from the ConfigMgr driving App-V persepctive.

Colin Millins for discovering the malformed Manifests.xml's, which breaks the processing of App-V packages.