Outlook, eVault.

You're talking about Vault Cache and Virtual Vault right?

So if the folder just disappears, the first thing to do is go to
File -> Enterprise Vault -> Configure Vault Cache (Outlook 2013)
or Tools -> Enterprise Vault -> Configure Vault Cache (Outlook 2007/2010)

Click the "Virtual Vault" tab, and you should see a checkbox when the available virtual vaults.
Check the user and press OK and virtual vault should now show in the left hand side

If the user isn't listed, then see what happens when you try and synchronize Vault Cache, either through the Tools menu, or on the Enterprise Vault ribbon or Synchronize Vault Cache button on the tool bar

It should show success , however if it fails, then you might need to determine why it failed.
If you're on EV10, you can try going to 

http://yourEVServer/EnterpriseVault/ClientDiagnostics.aspx and see if the user is listed there
You may want to check the include successful synchronizations as well

This page will tell you what stage they were at and whether it was succesful or not.

Other things i've seen mess up the displaying of Virtual Vault are

1. EVMSP32.DLL is not registered in the MAPISVC.INF properly
The EV Client when its installed updates the MAPISVC.INF with the EVMSP details, this is how the client and Outlook know what to display and how to display it. Sometimes if you uninstall and reinstall Outlook, the MAPISVC.INF is replaced and removes the entry.

A simple fix would be to run ResetEVClient.exe with elevated priveliges on the client machine

2. User NOT in cached exchange mode but the policy saying that it has to use the cache
You can either change the policy to not require the Offline Store (OST) or you can set the outlook profile to be in cached mode

3. The EV Hidden message is out of sync/missing/corrupt in the OST
I've seen a lot of odd behavior when the EV Filter messages aren't synchronized down to the OST correctly and then Virtual Vault either disappears or doesn't work or throws permissions errors

You can either run ScanOST.exe in Outlook 2003/2007, or you can d a Detect and Repair in Outlook 2010, or you can come out of cached mode, restart outlook, and then enable cached mode again.and await for it to say all folders are up to date, restart outlook and synch your vault cache again

4. The RPC Over HTTP Restrictions in the Desktop Policy prevent Vault Cache
Outlook will a lot of the time default to use Outlook Anywhere when it detects a slow connection to where HTTP calls are more preferable than RPC calls. But the default behavior within EV is when Outlook Anywhre or RPC over HTTP is enabled, to disable the client.

There are a number of options in the desktop policy though, give the client full functionality, disable the client, disable vault cache synchronization etc. So you can either change the policy, or remove the outlook anywhere setting. However, the outlook anywhere setting will most likely come back, unless you're on Exchange 2013 where you can actually disable the Outlook anywhere from being turned on automatically

These are just a few things i can think off the top of my head.
That being said, the definitive answer would be in the EV Client logs