I had a few months ago similar percent indicator problems. My battery from 100% drop in seconds to 1% and stuck here until switch drain battery. Also hekate also reported inaccurate battery capacity (mAh value). Somewhere on the web, mayby on reddit or xda, I dont remember now. I found, it is a normal fuel gauge problem in battery powered devices, and tried tips from that thread.
What I did on previously switch:
1. I also use this re-calibration payload - without success, still problems occur
2. Used a random .te script that I found on internet to also force reset fuel gauge - without success
3. Flashed pure backup of HOS from my switch that I created directly after got from box - without success
4. Ordered and replaced battery - without success too. On new battery I still had this problem ...
5. I dont remember more, but I really did some weird magic here
6. Found solution that worked on my switch, and on my old Samsung Note 4 too - its weird, but it had same problem later. I describe it below, what I remember, dont ask for link, I cant find it now again
I dont know how harmfull this solution is for battery life, but I dont noticed any changes in SoT
The solution for me, was easy but it is time consuming, you need to be patient, what I did:
1. From hekate (if you use hardware mod as I) run stock system, without mods, atmosphere etc.
2. Go to options and set Auto-Sleep option to: Never,
3. Set screen brightness to minimum - for slowly depleting battery
4. Leave switch and dont touch it anymore until battery was depleted and switch powers off
5. When batery is depleted and switch is off, wait a half of hour until you plug a charger.
6. Plug charger, power on switch to HOS menu dont touch, I mean dont play, and wait until full, but it need to be true full, when it hit 100% this can be a incorrect reading, just leave a plugged switch for 8-10h, after that:
7. Unplug from charger, AND power off.
8. Leave (powered off) switch for half or one hour.
9. Power on switch after this time and do steps 3-9 up to 5 times.
I did it 3 times and was enought for my switch, fuel gauge back to report true values in % and in mAh in Hekate
After this operation dont forget enable back Auto-Sleep.
I believe it will help you. I did this on two different devices (Switch and Note 4 and it worked for me fine)
Greetings