Hacking CIA and eShop

[Uncle_Iroh]

This may have been asked before, but I couldn't find it (the search function didn't allow me) so I'm asking here. What exactly is the deal with CIAs and the eShop? I thought that once you have CIAs, any time you went to the eShop, all installed CIAs would get deleted. What happened to me now was weird.

I had 3 CIAs, BigBlueMenu, Pokemon Y and 63 themes.
I installed an update to Pokemon Y via eShop (but I did a direct download, not a "go to eShop and view download").
My themes are gone, but the other two are still present.

Can someone explain this?

Also, how would I go about installing Pokemon Bank so that it works with both my Pokemon Y CIA and Pokemon OmegaRuby retails cart (that I run in classic mode)?

 

[cearp]

This may have been asked before, but I couldn't find it (the search function didn't allow me) so I'm asking here. What exactly is the deal with CIAs and the eShop? I thought that once you have CIAs, any time you went to the eShop, all installed CIAs would get deleted. What happened to me now was weird.

I had 3 CIAs, BigBlueMenu, Pokemon Y and 63 themes.
I installed an update to Pokemon Y via eShop (but I did a direct download, not a "go to eShop and view download").
My themes are gone, but the other two are still present.

Can someone explain this?

Also, how would I go about installing Pokemon Bank so that it works with both my Pokemon Y CIA and Pokemon OmegaRuby retails cart (that I run in classic mode)?

i think only dlc is automatically removed when you enter the eshop. (themes are dlc)
i'm not sure why games/apps are not, but, at least they are not, right

 

[Obi123]

Paid contents actually