I'm tinkering around with making the excellent SinsModCheck python script from the SGI guys work against other mods.
It doesn't run completely against Ascendancy, but it did report some duplicate entries. I doubt these affect Sins as it will either take the first or last duplicate entry (not sure which) and move on, but it will affect maintainability. Someone changing one of these might be sure it was changed properly, but still not see the expected behaviour in Sins.
** Reviewing Entity Manifest **
Duplicate entry in entity.manifest: Remnant_Daala.entity
Duplicate entry in entity.manifest: EotH_Oto.entity
Duplicate entry in entity.manifest: EotH_Stent.entity
Duplicate entry in entity.manifest: Remnant_Pellaeon.entity
Duplicate entry in entity.manifest: BuffRhazersEdgeTarget.entity
Duplicate entry in entity.manifest: AbilityRepairDroids.entity
Duplicate entry in entity.manifest: AbilityShieldRestore.entity
Duplicate entry in entity.manifest: BuffAntiMatterDetonate.entity
Duplicate entry in entity.manifest: BuffRepairDroids.entity
Duplicate entry in entity.manifest: PlanetBonusAcidAtmosphere.entity
Duplicate entry in entity.manifest: PlanetBonusCavernSystem.entity
** Reviewing Brush Counts **
Duplicate Brush entry: HUDABILITYICON_SUPERLASER in .\Window\HUDIcon-AscAbilities.brushes
Duplicate Brush entry: HUDABILITYICON_INTERDICT in .\Window\HUDIcon-AscAbilities.brushes
Duplicate Brush entry: HUDICON_RESEARCHSUBJECT_PACTUNLOCK_MARKET in .\Window\HUDIcon-Research.brushes
Duplicate Brush entry: HUDICON_NAVALCOMMAND in .\Window\HUDIcon-Ship.brushes
Duplicate Brush entry: MAINVIEWICON_NEBULA in .\Window\HUDIcon-Ship.brushes
Duplicate Brush entry: MAINVIEWICON_MC90 in .\Window\HUDIcon-Ship.brushes
Duplicate Brush entry: GameOptionsAlliedVictoryEnabled in .\Window\Screen-FrontEnd.brushes
Duplicate Brush entry: GameOptionsAlliedVictoryDisabled in .\Window\Screen-FrontEnd.brushes