This solution may help someone so sharing it.
We got errors engine metadata is not available for both methods (automated script and manual).
[PS] C:\>.\Reset-ScanEngineVersion.ps1
[exchange-server] Stopping services...
Stop-Service : Time out has expired and the operation has not been completed.
[exchange-server] Removing Microsoft engine folder...
[exchange-server] Emptying metadata folder...
[exchange-server] Starting services...
[exchange-server] Starting engine update...
Running as [domain\username]
--------
Connecting to [exchange-server]
WARNING: Unable to process update request because engine metadata is not available. Attempting to synchronize
metadata. Please try to run the cmdlet again later.
Dispatched remote command. Start-EngineUpdate -UpdatePath http://amupdatedl.microsoft.com/server/amupdate
--------
[PS] E:\Program Files\Microsoft\Exchange Server\V15\Scripts>.\Update-MalwareFilteringServer.ps1 [exchange-server]
Running as [domain\username].
--------
Connecting to [exchange-server].
WARNING: Unable to process update request because engine metadata is not available. Attempting to synchronize
metadata. Please try to run the cmdlet again later.
Dispatched remote command. Start-EngineUpdate -UpdatePath http://amupdatedl.microsoft.com/server/amupdate
Solution/Workaround
1. copy msvcr110.dll from c:\windows\system32 to %ProgramFiles%\Microsoft\Exchange Server\V15\FIP-FS\Bin and %ProgramFiles%\Microsoft\Exchange Server\V15\Bin
2. restart the exchange server
3. Use either automated script or manual method