The book folders are within the library, viz:
If you remove the book its folder is deleted from the library.
Would it be feasible to split the books into two files, one containing the Latin/Greek text the other the English translation. I do this with heavily footnoted text, so that I read the text and the footnotes alongside one another.
If that's feasible we can discuss how you might store the two parts in a calibre library.
Which operating system do you use - Windows, MacOS or Linux?
BR