Hopefully this wish isn't asking for tons of work making it have a better chance of existing... in the 'books with missing files' area would it be sane to have a 'mark all missing as read' in the menu? Or 'mark all missing as...' that presents a quick dialog with the 3 possibilities as buttons?
The main issue I have that causes me to ask for this, is when you have a dozen or so books that you've deleted via a reader as they are read, going into each book's view and marking them as read is a bit of a pain (in my case mainly due to the dropdown being too small to manipulate quickly even on an 8 inch screen.)
An alternate idea that would serve in my case would be to dispose of the read dropdown and put 3 buttons in a line ([o yes] [x no] [x none]) the size of the current dropdown's height, with the current one highlighted or radio buttoned making it easier to finger mash quickly.
I recently properly learned search in calibre (not #read:yes) so at least I no longer have to sync twice (before and after remove deleted files to tag as read.) This last bit would be icing on the cake for me at this point
Either way, thanks for CC!