I use Qt Creator installed using the online installer, and have Qt 5.9.3 for Linux desktop installed.
I have two kits configured in Qt Creator 4.5.2: The autodetected Desktop kit for 5.9.3, and another kit set up for an i.MX6 device running Linux. This Qt version (Qt 5.6.3) was built by me for the target device. The Qt Creator kit for this device is set up with it's own compiler, debugger, qt version and generic linux device.
My project is using Qbs. All works fine, building and running the desktop version locally on the computer, and building, deploying and running the i.MX6 version on the target device.
I then installed Qt Creator 4.6.0-rc1 in the online installer to try it out. When opening the same qbs project using this new version, Qbs warns "Module Qt.core could not be loaded" for each time it's depended upon in the project files when using the i.MX6 kit. (The autodetected Desktop kit works fine!)
I've also tried Qt Creator 4.6.0-beta1 earlier, but didn't try this project at that time. Just adding this in case that version somehow messed up some files.