I have been using the highlighter on scan PDF documents for over a year, not all of a sudden it is not working?

You can only use the highlighter tool on a scanned PDF it it underwent text recognition (OCR). Maybe the file you're currently using was not OCRed, and therefore you can't highlight it.

For more help you'll need to provide more information regarding the problem, starting with your application (including exact version), OS and the exact nature of the problem ("doesn't work" is not enough).