A free Mendeley account provides you with 500MB of space for your personal library documents and 500 MB for documents you share with other people. (You can purchase more space.) Because of this limitation, you may choose not to sync all the documents from your Mendeley Desktop to your Mendeley Web account.
These settings are controlled in the Mendeley Desktop application.
There is a Sync Library button in the Mendeley Desktop that will collect changes made in Mendeley Web and send changes to Mendeley Web.
Turning Syncing on and off can be done at the level of All Documents or per Folder/Collection. An Edit Settings button is visible when either All Documents or a Folder/Collection is selected; this allows you to toggle syncrhonization on and off.
By default, when you import a PDF, Mendeley does not move that file; it just creates a reference so it knows where to find that file on your computer. If you later move or delete that file, Mendeley will not be able to access it.
There are two ways to address this: