[@JohnSolaris][@Rex]
Assuming that this rp will be parallel to both shows (the events in Pokemon: Indigo League and Digimon S1), which it has been so far, harmful things to the human body are still "harmful".  

Take, for instance, whatever Koffing/Weezing uses frequently throughout (Smog, I think). It is a poison-type move, therefore possesses some poisonous attribute.  Yeah, the characters cough, hack, and have their visibility limited to about zero, but it does no lasting damage.  Therefore, I doubt "purging" will be an issue. 

By the same basis, temp in both Digimon and Pokemon have effects on real and digital beings.  Deserts cause characters physical discomfort, cold things feel cold, etc. regardless of whether they are digital or not.  Extremes can obviously cause death.  

Since we will be in the digital world, damage would most likely be handled by the same basis.  Digimon can be stabbed, shot, etc.  Though I doubt, regardless how strong the trainers digimon was, the trainers themselves could survive. Might be weird to scale survivability.  Though, admittedly, I cant think of anything better. 

Just some thoughts.