Anti-virus software on the server?
Are any actual documents being removed, or links broken?
Well...I figured out what I was doing wrong. My application has separate app and data files. My normal update process is to backup one or both from the externally hosted server then download them, make local updates, delete the server files then upload them to the server. Turns out that when I delete the data file on the server, the external secure file structure gets deleted too. Unfortunately, when I upload the data file to the server, the external file structure is not uploaded (it has to be manually installed by the hosting provider for FMS13).
Until the WebDirect server issues get resolved in FMS14 (which I hear may be resolved in FMS15), I'll change my process for making structural changes to the tables by connecting directly to the server copy and make the changes.
I hope this may help someone else avoid the frustration.
Your other options are to switch from external to internal storage before you download the files, or to copy the entire directory, including all the data files, down to your local drive, rename them, and then upload again.