unbalanced data bases

[ddouglass]

How much of the 6,000 and 5,000 are the same files?
I am guessing you are going to move the files to an external hard drive?
If you imported on both machines and didn't pay attention to your BookIDs then you probably have many duplicate IDs which will not rebuild without using the Merge Database. However this will change the duplicate BookID to the next available number. This means you will have to reprint your books to add the new items in.
I would copy the 6,000 to the new drive, then move it to the laptop. There are some utilities that you can use to compare the two drives to eliminate the duplicate files. Then copy the rest from the laptop to the external hard drive. After all of them are joined then do the Merge Database.