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That is pretty much by design. If you edit the files in between using the spell checker, hit refresh on the spellchecker. Otherwise, every time you do something with the spell checker it will have to reload all the files, on the chance that something changed, which would make it very slow. Remember that calibre's spell checker, unlike say Sigil's, has to parse the HTML files in order to understand which languages apply to which tags with the lang attribute. It does not do a simple search and replace.
That said, I will look into adding a check that will popup a message telling you to hit refresh when you click change word if some files have been edited since the last time you hit refresh. It never occurred to me that people would want to both keep the spell check dialog open and manually edit files at the same time.
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