Updated Version Reverts to Old Photos

I recently updated my Magazino theme and all the main page images reverted back to old images I was no longer using with the posts. These weren’t even uploaded as part of the posts anymore, and this was very strange. It took me quite a while to undo.

How do I avoid this particular problem in the future?

AND

How do I write code on some of the backend .php and .css pages so that no updates will override them? I fear this happening again.