Merge several folders, but keep only the newest file when conflicts are encountered
Just use rsync:

rsync -au .../src/ .../dest/
rsync -auiP .../src/ .../dest/ #if you need some visual output


and delete /src afterwards

with:  

-a, --archive               archive mode; same as -rlptgoD  
-u, --update                skip files that are newer on the receiver  
-i, --itemize-changes       output a change-summary for all updates  
-P                          same as --partial --progress  
                            --progress show progress during transfer  
                            --partial keep partially transferred files  


Please check man rsync for -rlptgoD