If you buy a flashcrd now, it can straightly work on 3DS V4.4.0 E/U/J console. You just install the latest r4 kernel and games into the root directory of the MicroSD card, put the r4 card with SD card into the 3DS console, then it works.
But if the r4 card in you hand is old version, which was released before 3DS V4.4.0 update, it need to be upgrade to fix the problem. (the firmware need to be refresh).
1. Update the r4 kernel in MicroSD card to latest version, as old kernel may be useless on 3DS V4.4.0.
2. Download V4.4.0 upgrade patch from official website, unzip it, and copy it into the root directory of the MicroSD card. (some r4 card may don't have this patch, as it was built into the latest kernel)..
3. Use a DS or Dsi console to upgrade the r4 card. There are 2 kinds of method. If the upgrade files is not built-in, you can open the MicroSD card in the DS, find the upgrade file and run it, then start upgrade process untill finish. If the upgrade file is built into the kernel, you just enter "r4 mainmenu" - "system config" - "upgrade" - "starrt", click the start key to start upgrade process untill finish.