As long as the amount of paper is negligible, it will still play.
Why not try to soak the cds in question in warm water to see if you can then get it all off?
What I'd be most concerned about (with that particular CD transport) is that it is slot loading. The loading mechanism may very well peel off some residual paper on the top of the CD as it sucks it into the unit. That might lead to issues in the future with little bits of dust and such getting into the unit and more importantly, cobbing up the loading mechanism.