There are problems, and then there are problems.
Grinding copper and then carbon steel on the same belt is asking for problems, as is grinding aluminum and then titanium, oir graphite and then titanium.
Carbon and stainless?
I don't know and, anyway, the final polishing should be made on a brand new belt to avoid excessive heating anyway.
BTW: there is no such thing as "stainless" steel. There are steels more or less resistant to oxidation but, given the right condition, any steel will rust.
Stainless just won't rust so easily, or so severely and deeply.
I've ground carbon and stainless on the same belt, and left the knives sitting on a shelf for two months in my shop, which always have one or two open doors and at least a couple of windows, and lots of humidity. Neither did rust. Why? Because I covered them with protective oil. I had my CRKT M16 rust after using it for eating Pizza because I left some tomato traces on the blade.
If you take care of your knife, it won't rust. If you neglect it, it will rust no matter what. So I wouldn't worry about anything like microparticles embedded in steel...
Just care for your knives as proper.
My experiencce in 20 years of knife using is that those who get rust on their knives DESERVE it.
It's that simple.