As far as I know, if you have files with same name/location but different content you have to explicitly select the action you want to do with those files before synchronization.
For example, select all files and hit CTRL+L, which will copy all the conflicting files from left to right panel after you hit Synchronize (which seems to be what you need, given that the files in the left panel are newer).
You can also choose other actions (just right click the file to see the list of options).