Case in point, at 2-A TD doesn't care much about barriers between Universes. For one there's the DBT beyond the infinite timelines which shouldn't interact with any timeline at all and not only can the thing affect timelines, dimensions and parallel universes while being within it, it can also leave and enter it at will (actually even any of the split weakened Dragons who are like a complete joke compared to its power are able to freely cross dimensions that are otherwise locked in all places making travel impossible save for one spot - and even they cannot reach the DBT. SERGE can't reach the DBT until getting like Three Macguffins, one of them channeling the TD's own power and the other interacting with Dimensions, etc etc).
That means the strategy that works against DD to prevent interactions between universes is not much help against the TD.
Plus I recently got my hands on part of a translation to some guides (such as Ultimania and the Missing Piece artbook) and they reinforced what I thought was just implied in the game (though Cal did remember me of that in a previous thread): That Lavos would be capable of absorbing Serge and the Chrono Cross had it not been defeated in order to achieve an even more evolved state of being superior to TD, so it's not outside its range of absorption to absorb a "2-A, possibly High 2-A" being.
Dragon's comment in the Harle thread pointed that All Delete nearly killed Yggdrasil, so while I won't say Existence+Non Existence Erasure could outright kill Mother Eater past that massive regenerative power (as Lavos lacks a feat of killing any High-Godly regenerator), I feel safe to say that ME could get damaged pretty badly by this, which at this point Lavos does by whatever it does, like even punching or something if way weaker playable characters hitting Non-Existent stuff are anything to go by.
TD Lavos is not a part of history at all (he literally exists in a place and/or state disconnected from all history and the infinite timelines as well) so I do have my doubts about Mother Eater creating copies of it - and even then, there should be alternates to make up for that.
Reformatting is good and all, but there are ways around it, Acausal alternates being one of them, which can't be stopped from happening in this case.
Most of the other things either cancel each other out or don't make much of a difference in the long run so I believe at this point, Mother Eater is actually outhaxxed to a degree, and if the likes of Omegamon can contend with it, it shouldn't have some massive gap in AP to make up for it. And having the Dragon God and Harle's spells and then some at this point also grants it some pretty problematic spells such as forcing properties upon the foe while giving himself the opposite property and changing the entire battlefield passively to whatever suits its needs for even further boosts in Stats while reducing the enemies' own. Furthermore, shifting stats effects inflicted on it to the enemy (meaning using Break fields to try and make up for statistic gaps would be shifted to Mother Eater via Revenge making it even worse).
There's also Stamina to consider, with Mother Eater having a High while Lavos is limitless since Base.
I believe TD safely wins this by those reasons, via outlasting, attacking it until it is weakened enough and absorbing Mother Eater in the end, as it seems to have more offensive and defensive tools to stay in the fight and an Absorption powerful enough to do it. Dunno how long it takes, tho.