@
clittle - I think the
Find Duplicates Plugin - Find Library Duplicates function can go a long way to helping you remove the duplicates from one of your libraries, prior to merging the two libraries.
Find Duplicates Plug-in discussion thread - the first post has an excellent summary of current plugin functionality. The Find Library Duplicates function was introduced on July 20th 2012.
One you've done with finding and deleting duplicates then you should use Calibres
Copy to Library feature to merge the two libraries.
BR