What is your version of InDesign?
What is your version of OS?
Are you working with documents from a server system?
InDesign CC2015 / Mac OS 10.10.4 / not on a server, an individual computer.
However, I found later, that I do have 2 La Cie hard drives attached to it, and the "blank folders" were on one, but it had actually packaged the files to the second La Cie. Which is kind of weird, because I had specifically chosen the one where the blank folders ended up. I have had issues over the last few days with InDesign "losing a bunch of work on files" ... when I left for a while, upon coming back, the files were closed (I hadn't closed them myself) and it couldn't "find" them. When reopening, it was to an earlier saved version - not where I had left off working. So I think there might be more going on. I did just replace the preferences, so I am interested to see if that does the trick.
I just did this - will see if that helps.