It is always good to maintain multiple copies of your website files. It helps having one version with you which is always similar to your online version.
If you have difficulty while moving files from one folder to the other, thinking that one version might be over-written with another…. try Examdiff Pro. This online marketing tool is a file and folder comparison software that has a beautiful interface. The two-pane structure helps you compare files easily and color coding where changes exist helps you to find the changes easily.
The comparison algorithm is also good and updated. Try the trial version or buy it for $35.
And synchronize away…..