When you edit > copy/paste a link/shortcut to a file into another folder on Vault's thick client it does not appear on the web client.
In a large company where licenses may be an issue the web client is ideal and should include links to drawings so people can access these drawings easily from different folders. In our case we asbolutely have to refrain from using this feature due to its in ability to appear in the web client. This limits the folder structure within Vault.
Ensure that edit > copy/paste shortcuts to files appear in the web client as well as the full / thick client.