Could you detail what is exactly the issue? Be careful to use the same codification in all your files in LaTeX. For me is easier to use always UTF8 (but not utf8x). With JabRef I setup the same encoding by default. But be aware that bibtex uses ascii but not utf8. here is a compiler a kind of extension of bibtex that recognizes utf8. Since I use LaTeX I don't need to use the old ascii tricks in my databases within JabRef, but it depends of the workflow you use.
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