Today,r4i-sdhc team released this update news that now r4i-sdhc 3ds card can work on 3ds v2.0 as well.Cheers,thanks for their hard work.
Here is the detail guide on how to update
By means of WIFI
As we knew,r4i-sdhc 3DS Supports updating kernel by wifi,so use WIFI-ENGINE and it will automatically download the update firmware to the root directory of your TF card.
Update by hand
you can follow these steps,i quote it from original unzip readme file:
1. You can not upgrade N3DS Card with N3DS V2.0.0. If your N3DS console has already been upgraded to N3DS V2.0.0, you will need another NDSL or NDSi or N3DS(which should be under version V2.0.0) to upgrade your 3DS flash card.
2. make sure nds fully charged, better with external power pluged.
3. First, reformatting the SD, download the latest kernel 1.40b.
4. Unzip and copy the files(R4iMenu,moonshl2,moonmemo,r4.DAT) to the root of MicroSD card.
5. Download the latest upgrading programs. Unzip and copy the file(fwupv20a.nds) to the root of MicroSD card.
6. Insert MicroSD card into r4i 3DS card, insert 3DS card into nds\dsl\dsi\dsixl\3DS
7. Turn on console and press "A" button to run the upgrade file fwupv20a.nds.
Note:When upgrading the r4i 3DS card, it is not allowed to turn off power or pull out r4i 3DS,otherwise it will damage the r4i 3DS card.
IF your 3DS is still in old firmware , just feel free to update the patch and install it.
Choose any one way that convenience for you and you will success in updating R4isdhc 3ds for N3DS V2.0.0