*Thanks everyone for their helpful comments. Finally, I was able to find a problem in the Better BibTeX. Some update must have caused the export settings to go off. It disabled the "Export unicode as plaint-latex commands" option. Pretty bad bug, I think. This together with my document not being set to utf8 caused a mess.*
Last release of BBT was 18 days ago, so if some update was a cause it wasn't necessarily BBT. If there's a problem in BBT, please report on the github issue tracker. I currently can't think of a place in BBT that even could change settings -- not even the preferences pane. Those changes are managed by the base platform that Zotero builds on.
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