Change how Citrix XenApp maps drive letters

I found a solution to my issue, turns out I had not been searching for the correct magic phrase. What I was looking for is under the pass-through client.

http://support.citrix.com/article/CTX238200

Client drive mapping on the pass-through client was restricted to the drives on the client device. The client could not map local or network drives configured on the MetaFrame server in a pass-through session. Local or network drives configured on the MetaFrame server can now be mapped by the pass-through client.

For version 10.xx

1. Run Regedit.

2. Navigate to: HKEY_LOCAL_MACHINE\SOFTWARE\Citrix\ICA Client\Engine\Configuration\Advanced\Modules\ClientDrive

Create the Reg Value: NativeDriveMapping

Reg Type: REG_SZ

Add the Value: True

When this flag is set, the client drives on the client device are not mapped and are not available. The drives configured on the MetaFrame server are mapped and are available to the pass-through client.

It almost sounds like this is a by-product of your folder-redirection policy. Folder redirection policies have the option to move the files to the new location. I seems as if you have this option enabled.