Correct. NOOBS is one of many variants of Linux that will run on a Pi. You overwrote NOOBS with Debian, another popular variant that the developers chose to develop Stratux with. If you learn to SSH into the Pi (which is not a requirement to use Stratux), you'll see that there are a LOT more Linux files on that disk, written in another partition, that the Windows computer doesnt/cannot see. That's also where you'll find the log files and other system files.
Also realize that any customizations are lost with each new image copy.