I was updating on a site that has approximately 250 menu items. The goal was to update the WordPress install, Plugins, Genesis Framework and move to the responsive version of the theme. I knew the original site had been customized so I decided to work on a staging site where I could do all the updates and customizations. For staging, I used the WP Stagecoach which worked extremely well.
All was fine on staging and I completed the customizations and then prepared to move everything over to the live site. All seemed OK until I noticed that more than half the menu items were missing! I tried to add items into the menu but it could not be saved. I then deleted some menu items and was able to add new ones and save the menu. However, once I reached the same number as had been in the menu, the menu stopped saving again.
A little research indicated that I had reached a limit on the number of posted variables and the php.ini file needed to be modified to increase the allowance. In this case, we had the host set max input vars to 5000. This solved the saving issue but I still had to get all those menu items in place!