Maybe it will be easier to do it via trait rather than via building. I mean, EB already has special traits like "Conqueror of Persepolis" etc. so you only need to add a script that would give the general who just conquered such a "capital/treasury" city the money boost and money penalty to the origainal owning faction. The trigger should be adapted to ensure that the whole event takes place only once.

Example: 1.- Antiocheia is the treasury city of Arche Seleukeia.
2.- Antiocheia is captured by the Ptolemies - Ptolemies get the reward, AS get the penalty
3.- Antiocheia is captured by AS - nothing happens (the treasury is already transferred to Alexndreia)

I am now not in the position to study the EDCT and EBBS files in detail, but generally it seems to me as comparatively easily doable (as a minimod to EB 1.1 - I still do not own M2TW). Buildings might prove little bit more trickier...