Are you using Paratext 7 or 8? I have never heard of the footnote insertion function in PT using \fk instead of \fq . When you highlight a word or phrase in the text and create a footnote, that word or phrase is automatically placed after \fq and followed by \ft . I do not know how you can make Paratext use \fk rather than \fq .
The reason your \fq is red is because of an error in your style sheet. I assume you are either using usfm.sty and a custom.sty style sheet (recommended), or have associated the project with your own non-standard style sheet in the project’s advanced settings. It sounds like you need to fix the style sheet.
I am curious why you want to use \fk . \fk means key word and would normally not be the default way one would mark quoted text in a footnote. By default such words are simply quoted text, which is why PT marks them \fq . If you want the word to also be bold then you just need to style \fq as bold-italic. If you want to mark it as a word in the glossary you should tag it with \+w …\+w* “glossary term”. Paratext will then check to make sure it is in the glossary and create hyperlinks to the glossary entry in the USX.
By the way, I doubt deleting the books will solve your issue.