How to Merge the Contents of Two Folders in Lion, Keeping the Newer Versions of Duplicate Files.
Select and copy all the contents of the folder containing the newer files. Paste the files ONTO the folder containing the older files. The unique files will be copied into the older folder without further ado. For the duplicates, a window will appear warning that a file with the same name already exists in the older folder. Check the "Apply to All" box and click on the Replace button, not the Skip button. These steps will merge all the files in the newer folder into the older folder, replacing the duplicates with the copies from the newer folder.
Unfortunately, the only information that the warning window provides about the duplicates is their common name, not sizes, dates, or times. These steps worked for me because I knew for certain that all the newer files were in one folder.
Mac OS X (10.7), iMacs, MacBook, and iPhone 4