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Sorry. I can't see implementing persistent checkboxes for the files in Book Browser to basically serve the identical purpose of searching only selected files. I know you say "losing the selections" happens too easily, but that can be solved by changing your workflow to make the selection of files be the last thing you check before searching.
It could be just as easy to forget you closed a tab or two before initiating a new search in my opinion. So I'm not certain how using the open tabs for the scope of a search would be any more intuitive than using checkboxes in Book Browser, or the already existing "Selected Files." It's all going to come down to a user training themselves to make sure they have the scope on their search nailed down before they search no matter which method is used. And we can't do that for them.
Sorry, but I'm afraid changes to S&R's scope(s) isn't in the cards right now.
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