i still don’t understand what i need to do with it!
You do not need to do anything with your database. Just leave it alone!
this is why i think it needs restoring
Highly improbable. The widget box disappeared because you changed themes. Widgets are stored on a per-theme basis.
it’s advising me as i might lose everything!
No. The notice advises you to backup your database before upgrading just in case there is an upgrade problem. With thousands of upgrades happening every day, it’s not surprising that 1 or 2 fail to fully complete. Backing up before an upgrade is just Good Practice ™.
The info in the file manager index.php is the current one
Current what?
obviously these files are not saves but just update as the site changes!
Obviously, you really do have no idea how WordPress works. It does not save your site’s content or settings in files! Take it from someone who has been working with, and developing in, WordPress for over 7 years. Before you go any further, I strongly advise you to read WordPress_Semantics so that you get an overview of the CMS that you are using.