Dithering is disabled by default on the latest nightly builds.
There's no need to uninstall .cia builds, reinstalling works fine.
When updating a single core, just reinstall the .cia with FBI.
When updating all cores and assets, it will be the easiest to uninstall every core and start from scratch letting retroarch install the cores upon loading them. ( install and run at least one core before placing back your backups )
On a side note, i did notice there's already made some work towards having network functionality on the 3ds builds.
I guess with some more work, online updating functionality could be added.
With all the cores being added lately, this may be useful since the current builds surpasses 400mb. Being able to just download the required core upon loading them would be a great addition.
With the rzip_stream functionality added, some of the menu assets and info files could be bundled and compressed to work around the slow SD's I/O speeds.
There's still some room for improvement, i'd say.