> Use a diff-datfile then. Use mamediff to create one.

As Roman says, MAMEDiff was defined for that very purpose. You should use -d1 (changes) or -d2 (supplement) in combination with your set type (-s=split merged, -m=fully merged, -n=non-merged). -d1 gives differences as full ZIPs (so that they can be copied over previous ZIPs) and -d2 gives partial ZIPs that in addition to the original ones are 100% complete and playable (can be used for a full rebuild too). Using -d2 you can have the 2 DVDs in your ROM path and 'supplement' directories for each subsequent version (90, 91, 92, etc).

You can either use MAMEDiff yourself or wait for me to release my data files each version.