To be honest (sometimes), I have no clue how Logos does highlighting anymore.
Nor do I care, since, in addition to 3 versions of Logos highlighting, I also use 3 versions of Kindle, Accordance (2 versions), plus Olivetree and Laridian. Plus of course 4 versions of PDF software. I just have no patience with cutie designs that are irregular and unintuitive.
In this case, the tip is that if you use Biblia and you're not really a Biblia person, your highlights in spanish are going to 'leak' back into Logos5 (in spanish of course) and thense wildly propagate in an unexpected fashion.
Apparently the highlighting can get started on resource-specific, even though you already have a single highlighting file. Or maybe ... who knows, there's no manuals.
I'm somewhat amused though, since periodically I just delete all my notes files, solving the confusion in a simple way.