be specific on WordPress and weaver II version (should be 2.1.10)
If you are using WordPress Custom Menus in Appearance > menus and you are saying that when you go back in there items are gone, this is a WordPress issue.
I remember someone mentioning a problem when you have a LOT of menu items and having to change some WP settings in that case.
http://forum.weavertheme.com/discussion/6924/menu-broken-with-wp-3-6weaver-please-help#Item_10
If you don’t have a particularly large number of menus / items, you may want to try and redo the WP 3.9 update from Dashboard > Updates
Hi, I reinstalled 3.9 and will see if this helps. I don’t have too many items. I will respond if it has not deleted again after a few days.
Thanks,
Peter