Originally Posted by CPH-Flyer

Even though it is separate tickets SK should be able to check your luggage through to your final destination, and being within the EU you clear customs in BRU, and your luggage is automatically forwarded. It should not matter whether you check luggage or not.
There is in the SK forum a post (a year or more back) that shows an internal instruction that staff should protect an SK to SK connection even if on separate tickets. I can't remember though if it made reference to domestic only.
1 hour is above MCT from non Schengen to Schengen on SK so in general, it should be OK.