In one of the recent updates (I use the term "recent" very loosely, it might have been as many as six months ago) this had happened with a lot of the sites when upgrading.  Obviously yours was not an upgrade but rather a migration... but I would imagine it follows the same reasoning.  Basically some things are cached "wrong" and completely restarting the website or app pool causes the application to completely restart, clear all cache, and start over from scratch.  I had it happen on 3 out of 6 sites I upgraded when the patch I talk about happened, so it was somewhat random but certainly common.

I too had this problem, also no migration or upgrading. I wanted to try restarting the app pool as suggested in a previous post, but no menu, no access to the DNN "Restart Application" link. The shared hosting provider objected, actually refused, to restart the app pool. Then I remembered the modify-the-web.config trick. That got DNN restarted and the menu items reappeared.

So, the answer to Cyrelle's post is to modify the web.config file (just add a space somewhere, any modification to the file). Changing the web.config file triggers a restart of the app pool.