Note that the _chk variants of longjmp come from <bits/setjmp2.h>, which definitely shouldn't be included if __USE_FORTIFY_LEVEL is 0 (i.e., -U_FORTIFY_SOURCE).
It's been a while since I meddled with KO's buildsystem, but there might be some parts of the build that don't yet honor every flag we enforce, in which case, if you can pinpoint the root issue, send a PR on GH.
That said, a cursory glance at the Makefile doesn't reveal anything wonky on that front for crengine...
Double check how your're setting your *FLAGS, and the sanity of the headers of your TC. I'm guessing you weren't using the kindle-legacy target?
@knc1: Technically, it's a fork of the ancestor of KOReader, kindlepdfviewer
.