If the 3DS updated and blocked the flash cart, it's not going to work until the cart gets updated or replaced.
Also there's no 3DS emulators, period.
The page for my card says that it supports 5.1.0-11E perfectly.
EDIT: The page says the following:
"R4i-sdhc 3ds card marked with "v5.0" and "v4.5" and "RTS" which can support N3DS V5.1.0-11 and NDSi v1.4.5 perfectly, please update the firmware to V1.67b. [2013-04-08]"