When I say GOOD CIA, I mean a cia that will not interfere with eshop
downloads.
For example, download a GOOD CIA of an update. In the future, that update can gets updated. You download the new update from eshop, it installs fine.
You can delete the installed game if you want, and still redownload it via eshop!
With a BAD CIA (like from plaicdn), eshop will give you an error at 99% if you try to update/redownload via eshop.