What i believe, is that the eshop only allows you at one eshop at a time, on my o3ds, I region changed my us 3ds to europe 3ds and the eshop worked, (SecureInfo_A was from someone else). But then i region changed from europe to japan and eshop didn't work. I did a method to make the eshop work on region changed consoles and the eshop worked. But then i tried to go back to the europe eshop and it didn't work.
You do have to do the swap trick each time you change your eShop region, so yes, you can only be on one shop "at a time". However the problem with the New 3DS is slightly different as EUR/JPN original region consoles have the added difficulty of preregistered titles to their CTCerts, so when you try to connect to a foreign eshop with the swap trick, it mostly works, but then fails to connect when it tries to get a ticket for a foreign title (JPN Flipnote Studio 3D, for example) that doesn't exist in that eShop.
This is why we have to try the extra patching step that yifan_lu suggested above where we would filter the SOAP responses rerouted through a local server (I want to attempt this eventually, but have already spent too much time on New 3DS hacking today, hopefully later this week). I encourage other people to experiment with these suggestions as well and please share your experiences!