Highlighting bug
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I got a bug this morning before sunrise where highlighting was removed from any locally downloaded documents when opened in Pages or Preview (.docx), and even if uploaded to Google Drive and viewed. Later in the morning, some time after sunrise, I noticed that highlighting was working again – I was able to view previous highlights in a document that I couldn't view before sunrise. For the record, I didn't knowingly restart any processes, nor did I log out or even quit f.lux between when it wasn't working and when it was working.
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What was the color temperature in f.lux?
You see, I think it was due to the color temperature being so warm and red that it actually made the highlighting become impossible to see due to the color of the highlighting mixed with the color temperature from f.lux. I think that's why you could see the highlighting after sunrise. After all, after sunrise, the color temperature by default goes back to 6500K.
Try this: open a document that has highlighting. Then, open the f.lux window and slowly adjust the color temperature until it gets as warm and as red as you can possibly get it. I think you'll find that as you make the color temperature warmer, the highlighting becomes less and less visible and finally completely invisible.