Assuming you're not using arm9loaderhax type custom firmware...
Do a full rundown by checking the SD card, updating the CFW setup on the card and CTRNAND, and backing up your game saves+extdata & SysNAND. This post should troubleshoot most minor CFW issues.
This must be clear at first. Are you still on A9LH or is it really upgraded to B9S? Hold "Select" while booting to find out your Luma version like in the picture in this post.
If you really are on B9S, just follow TurdPooCharger's tutorial (link above). Step 5. has a link to the CFW starter kit which contains most (all?) you'll ever need. And... I know, nobody feels like doing this, but you should really do the full test before trusting the new SD.
Good. You have B9S. The last Luma version with A9LH support was 7.0.5. You will not harm the console buy setting up a new SD-card.
The SD test is just to ensure your card is not damaged and not fake like in this case. If the card is okay you will get "Test finished without errors". Any other result is bad.
Just follow the nice step-by-step guide from the link above.