Lost Changes

Am I missing something? I have been working on a project for a couple weeks now, have made many changes, always saving on exiting, everything has been operating fine.
I went to work on the project today, opened PHPRunner, none of the files were in the recent list, navigated to the projects folder, opened my file.phpr, on opening got a message that states" The following database tables has changed since you last saved this project --- Do you want to synchronize database and projects settings? "
The tables are in there, the fields look okay. Missing Custom views, custom SQL entries, Field orders and names, visual changes, themes, everything.
Regards!