Resuming An Incomplete Merge

1. In the preferences window, under the "Photo Copying" tab, check the "Don't import duplicates" checkbox. When you restart the merge, iPhoto Library Manager will check as it proceeds to see if the photos it's about to import already exist in the destination library and skip them if they do.
2. Also, check the "Combine contents of albums with same name" checkbox. During the first attempt at the merge, the albums from the source library were recreated in the destination library and any photos that have already been imported will already have been added to these albums. Checking this preferences will make sure that during the second part of the merge, instead of creating a whole new set of albums and adding the imported photos to them, it will instead add the imported photos to the albums created during the first merge attempt.
3. If you were experiencing stability or speed problems with iPhoto during the initial merge, you may also want to enable the "Relaunch iPhoto every N rolls" option. This will quit and reopen iPhoto periodically during the merge, which helps keep its memory footprint on the system low, and tends to increase the stability of the program as it's imported roll after roll of photos.
4. After setting this up, go ahead and do another merge with the source and destination library you were working with the first time through. iPhoto Library Manager will have to process the already imported rolls, checking for duplicates, but it should eventually get to the rolls that weren't imported the first time and start importing those photos.