The Secretary of Transportation serves as the pleasure of the Governor. Given that the incoming Governor voted against confirming him while she was a senator, it was a foregone conclusion that current Secretary Richard (not-N9JIG) Carlson would be leaving office. A blog post made this morning has now confirmed it.
http://kansastransportation.blogspot.com/2019/01/transportation-secretary-richard.html
No word yet on whom Governor-elect Kelly will nominate as the next Secretary of Transportation.
EDIT: See update below
UPDATE! An interim secretary has been named.
Quote from: AP
(Governor-elect Laura) Kelly also announced Wednesday that she is naming Julie Lorenz of Lenexa as interim transportation secretary.
Lorenz is a senior strategic consultant for the Kansas City engineering, planning and architectural firm Burns & McDonnell. She previously led strategic planning for the Kansas Department of Transportation.
I think (and a quick Google search appears to confirm) that Lorenz was in charge of the Economic Lifelines lobbying group for a couple of years in the early 2010's. On the whole, I think she is a good choice if Kelly would like to make the interim appointment permanent, since with T-WORKS coming to a close and KDOT on course to lose its ability to match federal funds fully in the next few years, strong advocacy will be required.