I'd keep the original, first-ever-made backup, just in case something else goes wrong in the future. But, make another NAND backup with the latest working firmware.
As for the reason, I'm not 100% sure but I wonder if restoring an older NAND backup and updating the firmware via Daybreak would be "clean" enough for Nintendo not to flag it for suspicious hacking activity and possibly ban your console afterwards. Therefore, restoring a newer backup should be far less of a problem as far as telemetry Nintendo collects goes.
For now, it doesn't hurt to make another backup, but do wait and see if someone else more knowledgeable replies,
@Draxzelex perhaps?
The correct process for trying to avoid a ban are as follows:
- Make a clean NAND backup before doing any other hacks/CFW/homebrew using Hekate including boot0/boot1 and raw eMMC GPP (which will become a rawnand.bin)
- Perform any and all hacking offline with the Wi-Fi settings deleted and Airplane Mode to prevent accidental connection to Nintendo Hotspots (think 3DS Spotpass)
- Restore the clean NAND backup as well as boot0/boot1 prior to going online
- Make another NAND backup as well as boot0/boot1 at this point since your NAND has made permanent changes while connected to Nintendo's servers that are not present in your original NAND backup
- Repeat steps 2-4
Taken from
this thread. If I got it right, you should make a NAND backup
before you make any hacking activity and
after any official online activity on it, which makes sense to me. Backup that you're restoring should the last one Nintendo "saw". Since you'll be using sysNAND for official stuff only and emuNAND for homebrew stuff only (with Internet access blocked and 90DNS / DNS MITM applied), I'd say that you don't need another backup unless you plan to "dirty" your sysNAND in one way or another.
. Mostly, it would save me from having to make a new backup 
