Been meaning to write this up for the community and post it since December 2021. Finally doing it.

What are we trying to achieve?
Run FileZilla Server as a Windows Service and assign FTP users home drive / share folders on the network drive.

Why am I doing this?
If you Google it, people say it can't be done or can be done but people still have issues. Or can be done but no clear guidance.

What tools do I need?
You will need the following

• Windows Server either running Core or Desktop experience. 
  Not tested on Windows 10/11, but should still work. 
• FileZilla Server.
  https://filezilla-project.org/download.php?type=server
• PsExec
  https://learn.microsoft.com/en-us/sysinternals/downloads/psexec

Target audience for this guide?
A computer savvy person that is comfortable with command line tools and interpreting technical documentation.

What is the issue with using mapped drives?
When FileZilla Server runs as a Windows Service, it cannot access the mapped drive. This is because the Windows Service runs in a different user context to the mapped drive. Ie, the FileZilla Server service runs as SYSTEM account, and mapped drive runs as your USER account.

The issue presents itself in the administration console in the following image.

Example of a FTP user set with the mapped drive as their home drive.

How do we achieve FileZilla Server running as a service with access to the mapped drive?
The FileZilla Server administrative console runs in your USER context. The FileZilla Server running as a service runs in the SYSTEM context. They cannot access each other's environment and mapped drive. But we can mirror the users environment to the system environment so they are exactly the same.

So when a user's FTP home drive is set to Z:\ via the user running FileZilla Server administrative console, the FileZilla Server service will also have access to the same mapped drive.

Guide to setting up FileZilla Server as a Service with Mapped Drive.
Install FileZilla Server and the administrative console. When prompted for service settings, "installed as service, started with Windows".

Map the network drive as the logged-on user, this needs to be the exact mapping we use later - drive mapped as persistent.

Start cmd.exe with elevated rights, change directory to where psexec.exe is stored, and launch with this command.

Psexec.exe -s -i cmd.exe

Double check you are running as SYSTEM.
Run command below

whoami

Add/cache the credentials into the SYSTEM account, this is required to access the network share with cmdkey.exe

We cache the credentials with cmdkey to store them securely, none of this passwords in plain text please. If you want to know more about cmdkey, Google "Credential Manager" as this is the gui version for logged-on users. We need the command line version cmdkey, because we need to add the credentials in the SYSTEM context.

Use this command line

CMDKEY /add:<ServerName> /user:"<DomainOrServerName>\UserNameToAccessShare" /pass:<ThePassword>

For example, the share you are trying to access is on computer StorageServer and the username to access is below.

JohnSmith
MyHiddenPassword

The command to cache the credentials is

CMDKEY /add:StorageServer /user:"StorageServer\JohnSmith" /pass:MyHiddenPassword

Check the key is added by running

CMDKEY /list

Next mapped the drive, to ensure you have access. Do not map drive as persistent, I tried this and the mapping did not persist between reboots.

NET USE Z: "\\StorageServer\NetworkDrives\FileZilla Server"

Access looks ok as SYSTEM, good to close/exit cmd.exe running as SYSTEM.

As the logged-on user, create a Task Scheduler to remap the drive at boot - remember I mentioned mapping the drive as persistent does not work, you need this task to map the drive on boot.

Create the Task with the following details. The by default it will set the task to run with your logged-on user account, change this to use the SYSTEM account.

 Search for "SYSTEM", not "NT AUTHORITY\SYSTEM" although it registers the account as such on submission.

Set the trigger with the following details.

Set the action with the following details. Remember, this must be the exact same path as we mapped as the logged-on user. Program/Script: cmd.exe

Arguments: /C NET USE Z: "\\StorageServer\NetworkDrives\FileZilla Server"

Once the action is added, it should appear as the following.

Set the conditions with the following details. Uncheck Start the task if only on AC Power.

Configuration is now complete.
All that needs to be done now is reboot and check the Task has run successfully. This can be done by viewing Task Scheduler and viewing the Last Run Time.

Task added and before reboot.

 Task after reboot.

If you really want to ensure the drive is mapped, you can use psexec.exe again to run as SYSTEM, and check for the map drive using NET USE.

Now is the time to test out the setup end to end. Start the FileZilla Server Administration console, and set a user's home drive to the mapped drive. Marvel what should have been a simple task finally finished.