On my main machine, I use Debian Jessie, which is testing, and I always put in the latest kernel. After a year or so, the updates become quite confused. I always know I'm in trouble when an update suddenly wants me to remove half of KDE.
I copy everything to the second disk, including the hidden files. Then I install the latest Debian testing. It's a pain reassembling all my programs, but they are all out there. Nice thing about Linux.
Now it's all working again.