Well, you'll loose your already installed apps if you reflash just the kernel. But you won't lose the majority of your configuration files or saved data for those apps, so when you reinstall them it'll be almost like it was.

Rather, I'm not sure if you can reflash just kernel files. As I understand it you either reflash rootfs (which has kernel, and some other system stuff), or rootfs and EMMC. I'm guessing the "reflash just kernel" mean the former.