Adding an altar upgrade recipe works correctly with:

mods.astralsorcery.Altar.addDiscoveryAltarRecipe(
	"astralsorcery:shaped/internal/altar/upgrade_tier_2", 
	<astralsorcery:blockaltar:1>, 700, 100, [
            null, null, null,
            null, <minecraft:grass>, null,
            null, null, null]);

Removing an altar upgrade recipe with the same registry key does not work:

mods.astralsorcery.Altar.removeAltarRecipe("astralsorcery:shaped/internal/altar/upgrade_tier_2");

With the error:

[AstralSorcery Altar Crafting] Could not find recipe to remove with name astralsorcery:shaped/internal/altar/upgrade_tier_2

The same thing happens with further upgrade tiers.

CraftTweaker: 4.1.11
Astral Sorcery: 1.10.3

You need to use a different name for the second recipe you want added. This was part of the changes, and is working as intended. All recipes need a distinct name now, and recipes with duplicate names are automatically removed to prevent needing to go through and remove before adding a new one.

Hmm, Crafttweaker removes all recipes first, then adds new ones, so it can't remove anything which is added by itself...
The original recipe name is "astralsorcery:shaped/internal/altar/upgrade_tier2" so no "_" between "tier" and "2" which works fine on my side.

Thank you both, issue resolved.