Hey guys, I just finished wiping free space with the latest Ccleaner v3.21.1767. I ran it on the 3 passes and never lost my restore points.
Like I said before, the last couple of versions haven't been touching the restore points. It really isn't Ccleaner that is or was the problem. When Windows registers that it is running low on space, it automatically starts deleting restore points.
I'm not sure how the problem was corrected, but it seems not to be occurring anymore. At least not for me.