I have changed my emunand region from 9.1J to 9.1U and then updated to 10.4U. Everything works fine except eshop of course but that a SecureInfo_A issue.
@Nazosan and I were working on this a week or so ago. You can't just install 9.1U over 9.1J. Too many things are missing and your emunand will be incomplete causing most of the errors you see(keyboard and things). Here's what you need to do.
1. Get all of the updates for the system region you want to switch to starting from the lowest you can find (4.2) to whatever your emunand is now (9.2). If you are using a N3DS get the O3DS updates up to 8.1 and then get the N3DS updates from 9.0 and up.
2. Merge all of the update cia's into a single folder overwriting older versions with newer versions (add 4.2 cia's to the folder then 4.5 cia's then 5.0 etc..) when you are done there should be around 170 files.
3. Delete all cia's starting with 0004001B, 0004800F, 00048005, 00040130, 00040138, and 00048005. These will prevent the emunand from loading.
4. Place all of these cia's in a folder named updates on the root of your sd card.
5. Use FBI to uninstall the main system titles from your emunand (system settings, mii maker, miiverse, camera, etc...). If you region change before deleting the system titles it will cause your emunand to freeze randomly and block you from entering the system settings app.
6. Use sysupdater in emunand to install all of the cia's in your update folder. When this is done your system will reset.
7. Use decrypt9 or rxtools to inject the SecureInfo_A for your new region into emunand. My system was weird in that I had a SecureInfo_B instead of A so rxtools would not work but decrypt9 did.
8. Congrats!! You have a region changed system. Now format it and update however you like. I updated with a cart to 9.4U first and then updated through system settings to 10.4U.
The eshop will not work unless you had a SecureInfo_A from a system that never connected to the internet.