I've done a few conversions to CMake, and none of them took longer than a weekend. The main issues were administrative (getting cmake installed on the build servers, making sure the continuous build continued to work.) The maintenance overhead of autotools is very, very, high, and you'll get back those two days and more in a few weeks. And you'll have a build system that you understand and have confidence in, rather than a black box.
I don't know much about QNX. I believe CMake supports it in some form, but they had trouble finding anyone who actually used QNX to do maintenance.