They tracked flawlessly, so it's incredibly frustrating to have them removed and have my ability to add them removed. I have to go through all spells in the game again to make sure I don't miss one of those, unless there is a way to tell which spells I had tracking before this update.

I want to suggest to you to add the ability to track all of them, but I can't do so if I no longer have access to my list of spells.

I'm so sorry, but unfortunately, I had to do this downgrade. With user-defined spells it was hard to provide updated cooldowns (there were merge conflicts). BTW I've tried to add all important spells on the start of Shadowlands, so maybe you'll find it sufficient.
If you have not backups, but you added your spells by spell id then they still in database. File located in <<World of Warcraft folder>>\_retail_\WTF\Account\<<account number>>\SavedVariables\NameplateCooldowns.lua. There will be text like

NameplateCooldownsAceDB = {
	["profileKeys"] = {
		_<profile keys>_
	},
	["profiles"] = {
		[_<profile name>_] = {
			...
			["SpellCDs"] = {
				[47585] = {
					["enabled"] = true,
				},
				[207777] = {
					["enabled"] = true,
				},
				[18499] = {
					["enabled"] = true,
				},

Numbers in square brackets are spell ids. There will be spells added by you and also default spells, so it would be hard to differentiate them. Sorry again.

Thanks for the answer. I've given up on knowing what I used to track and perhaps there are more that should be added, but I just skimmed the talent calculators on Wowhead and I would like these 27 cooldowns to be added if possible:

Death Knight: 1. Abomination Limb (covenant); 2. Wraith Walk

Demon Hunter: 1. The Hunt (covenant); 2. Eye Beam

Druid: 1. Convoke the Spirits (covenant); 2. Frenzied Regeneration

Hunter: 1. Resonating Arrow (covenant)

Mage: 1. Radiant Spark (covenant)

Paladin: 1. Ashen Hallow (covenant); 2. Shield of Vengeance

Priest: 1. Mindgames (covenant); 2. Mass Dispel; 3. Vampiric Embrace

Rogue: 1. Marked for Death; 2. Kidney Shot; 3. Gouge; 4. Between the Eyes

Shaman: 1. Stormkeeper; 2. Earthen Wall Totem

Warlock: 1. Soul Rot (covenant); 2. Dark Soul: Misery; 3. Dark Soul: Instability; 4. Havoc

Warrior: 1. Spear of Bastion (covenant); 2. Rallying Cry; 3. Intervene

Thank for your contribution! Spell list is updated in version 90002.3-release.

Wow, you added all of them! Thanks a ton; PvPers everywhere will rejoice and I get to feel cool like this is my update. :)

Hello, I've also ran into the problem with custom spells I used to track that are no longer there. Could you please add this when you have the chance? Thank you.

Paladin (Holy) - PvP Talent
Divine Favor
Spell ID: 210294
30 sec cooldown

https://www.wowhead.com/spell=210294/divine-favor

@ZoopGH Thank you for detailed description! Added in 90002.4-release.