Keeping continuity between multiple databases

[eluser]jleequeen[/eluser]
I brought up this question in a reply to another post, but thought it warranted one of it's own.

In a situation where you have multiple CI applications each running there own databases but those applications need to start talking to the other databases, what do you do? What is the best way to approach this?

Is it ok to alter the database of another app through the model from a separate application?