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As of 1.25 *all* metadata (except cover) is saved to PDF files. If metadata in your PDF files is not being updated, you most likely have either disabled the PDF metadata writer plugin in Preferences->Plugins, or the PDF files you are working with are somehow broken, so metadata update is failing. If it is the latter you can check by running calibre in debug mode and doing a save to disk.
As for adding books I cannot reproduce it, steps I tried:
1) Add a .txt file to calibre
2) Change the title to "Test title" author to "Something else" and series to "test series [3]"
3) Click save to disk. txt file alongwith opf is saved in a folder named else, Something/Test title
4) Click add books, multiple books per folder and choose the folder else, Something
5) Book is added with correct title, author and series
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