Saving metadata in the ebook file

Hello all. I'm relatively new to Calibre (though I did use it a bit a couple of years ago for minor library management) and I've come across a rough patch.

I'm attempting to update and correct the metadata in quite a few of the ebooks that I have and I can't figure out how to get Calibre to actually save that information in the actual ebook. Upon making changes to the metadata it saves covers in the folder with the book and the metadata in the .opf file. This would be fine, except I need these books to work with a reader that does not support getting the books from Calibre (at least I assume that if I used Megareader/Quickreader to import the books it would get the correct metadata).

I have selected and unselected each of the options in the Save to Disk section of the preferences, and it doesn't seem to work unless I actually export the books using the save to disk functionality. Seeing as I have a large collection and centralized management is a primary goal that is not an ideal solution (even re-importing after the export).

Is there any way to make Calibre save the metadata from the database into the file that Calibre has as the centralized managed copy?

Thanks for any and all help that comes my way with this issue.