I'm very confused as to how and why I lost a

[Arralen]

fatigue, damage and affictions:
Lemme see:
Earth mother has 55hp/turn regen, Def 8, Prot 19(!), MR 20

You're attacking with
3 Carrion Elephants .. 2x SleepVine (3Attacks , Dam 33Stun, Att 5, MR negates)
2 Carrion Bear ... 1x SleepVine, 1x Claw (Dam 17, Att 6)
1 Carrion Boar(?) .. 1x SleepVine (Att -2), 1x Bite (Att-1)
.. that gives you 30 attacks on her per turn.
The rest of you troops simply can't hit her as those above are blocking the way.

=> Question: Does fatigue over 100 still adds to defense reduction, or is it capped at -10 at 100 fatigue? Can effective defense go negativ through reduction by fatigue? In this case, the EM would wind up with -11Def instead of -2, or even only 0 ...

In the Last case, the Boars attacks would be negligible unless they are the very first to happen. In that case, they'll help you drive down the EMs defense value.

With 2 Dam17 attacks it's unlikely to do any real damage against her Prot of 19.

That leaves you with about 24 SleepVine attacks which are neither armor piercing nor ignoring. So they have to go through her Prot18 (plus 2 d6oe: lets say 26 on average ?!) to do their fixed damage (33, no d6oe roll here ?!).

24 attacks which do 7 pts of damage.
How many attacks are negated by the MR20 ?
One succesful attack is needed to drive her over 200 fatigue again. The other are going to do real damage.

Finally, she regenerates 55 hp/turn, or about another 8 attacks worth of damage. And with 238 hitpoints and regen, you won't see that much afflictions from Dam-7 attacks.


path finding
There is an -albeit small- issue with pathfinding, or two

The layout of Ermorian Citadel is the same (or similar) to the hill fortress (IIRC). The entry path is 2 wide only, while one could think it's 3 wide judging from the look of the buildings. And it is not where the terrain is flattest, but moved one row towards the spectator.

That means, you troops to the "south" (spectator side) simply could go around the EM because the where blocked by the wall/ the ramp besides the gate way.

That the Vine Ogre to the "north" didn't move was correct in so far, as they tried to attack the nearest enemy but where blocked by the Carrion Beasts.

They couldn't get around them because a) they would have had to go backwards after moving past the CBs (did I get that grammar right?), what units are very reluctant to do unless when routing. B) pathfinding is left-right orientated. You can try this out by spreading some slow-moving targets on the battle map and have a bunch of knights mop them up. As long as the knights are going left-right (back or forth from their pov), they'll happily spread out to the left and right of the target (their pov again). But if they have to traverse the battlefield, they'll string up one after another. And that's what happened to your Vine Ogres as well.

additional remarks
You have lost the game anyway. C'tis has enough troops to roll over you everywhere at once.
You're forging to many useless items. At least, useless on the commanders you give them to. An undead has fixed encumbrance=0, but spellcasting encumbrance suffers from enc-4 armor (result +8 enc) as with any other spellcaster. Stuffing spellcasters which are placed in the very back of the battlefield with melee gear does only makes sense if they are a)threatened by assassins and b)able to make use of it (which pans certainly are, ok).
With 234 astral, 119 death and 340 nature gems in the treasury you should summon much more upkeep-free troops and commanders. (Some Horned Serpent to poison the EM would have been great)
If you've got the Ettin Mandragora, you should stuff it to the teeth, err, bone and use it to force the way into any sieged castle. There are few things which could really block him. Maybe an EM could
And you have got the Harpy Queen, and lots of free harpies therefore. Bring them along, set them to "attack rearmost", or "archers" or something. That would make the defenders go for them, and sometime un-block the gate way.