Games : Does the Nintendo 3Ds System Transfer delete the data on the target system?

I want to do a system transfer, but I have different Nintendo IDs for my two systems and I've downloaded games on each of them.

I have quite a few questions because I'm confused with the info on the internet and on the actual systems during transfer:

1. 
   

   Will the data on the target system be deleted?

   
   


2. 
   

   If not, will the games from the source system be combined with the games on the target system? (Will I be able to play my source-system games, as well as target-system games, on my target system?); and what happens if I have the same game on both?

   
   


3. 
   

   If the games on the target system will be deleted but re-downloadable, does that mean my saves are gone? Is there anyway to keep the saves of my target-system games?

   
   

Thanks! :D