Encore should not ignore two of the timelines. Originally, what were the assets transcode settings? All automatic? It sounds like they may not have been. Or the disk may have been set to BD dual layer. Or you might have transcoded when only one timeline was in the project.
Are all 3 max 30 target 25? If you don't know at this stage, set each asset to "revert to original," then make sure they are set to "automatic," and transcode. Do you get the error? Then look at the datarate used.
The alternative is to use a bitrate calculator and the length of the timelines in minutes, and work it out with manual transcode settings.