I had a hell of a time with this problem too. What I finally came up with was this: Use the regular keyboard tilde but add subscript formatting to get it to appear at the middle of the character. You can also add bold to make it more visible after that. Like so many things in LyX you have to workaround it or spend 10 hrs learning some useless programming knowledge to solve a problem. Sorry this response is 3 years late ;_;
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