What yoyo did you do those flops on?
Mostly yoyos with harder axles like walnut (the recent standard) are very hard to scorch because they are so smooth and pretty dense. Try doing a long combo on a No Jive (or even better, a Russell) and you will smell smoke pretty quick. 
Also if it’s a yoyo you’ve played a lot, you take care of most of the wood imperfections anyway. It’s really just a new axle which is easy to destroy with friction. And even then we are t talking about cutting right through it - just burning a line/groove into it which increases contact area with the string and worsens play.