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Highlight some text
See what Language it's in via the Character dialog box
Someone may have inadvertently change the language of the document, this language setting is what's used for the spelling only.
Ended up having the same issue in a CC version document. A combination of fixing the Language setting on character styles and editing Preferences, Dictionary, Spelling and also Hyphenation to Hunspell did the trick.
It should be noted that both of these problem files were ones that were being shared and edited by two people via dropbox. I'm guessing that the preferences are not set correctly within InDesign by the other user, thus resulting in what you noted above as a change in the language associated with the file. A cautionary tale for anyone working with a client who may be doing some content editing on a shared file, as it seems settings overwrite.
Language setting are per document for this type of thing.