Last time the Contents.acp file had to be merged, Alan Davis had to work out what changes had just been made to the files in each zip and then merge them in an exploded directory, so nothing is lost. It is a real pain. You have to work out what changed on each branch and then make the same changes to the other. diff is not enough. An easier way would be to not store them as zips but build them as zips.
I'm not sure of the implications of this change, but an investigation is worthwhile.