Hi Pioneer,
Yes, we always have our sites updated to the latest version of WP.
Our loss of widget areas happens frequently when we move from our development server to our live server. In this case, the domain name is always changed. We run an SQL script to change the name where it exists in the database.
Our theme is based on the loop with a few features that we put on every site. Namely, a mobile menu system.
The last few instances of widget disappearance have happened on live sites with no recent updates or changes. This seeming randomness is what is throwing us a curve ball.