This is the primary issue I've found with using ECOs that can control the release of more than one drawing/document. Apparently, the out of the box ECO capability or EPDM is limited to those systems wherein each and every ECO releases one drawing -|- and each drawing requires its own ECO. That's certainly a workable if clumsy method, but I've never worked in a company where this strategy was pursued. It always makes much more sense to review and release related groups of drawings together, and that's the way we do it as well.
The main problem stems from the fact that EPDM does not provide a mechanism for distinguishing between SW references (created as a result of components being inserted into assemblies) and EPDM references (created using Paste As Reference). EPDM views them as identical, and so it can't perform a transition on referenced files without acting on all referenced files, regardless of how that reference was created or what it represents to you.
AFAIK, there is no way around this limitation except through some sort of custom programming solution - except for using the one ECO per drawing paradigm.