On Window, when there is a conflict between folders in a copy operation, the replace option simply merges the folders and overwrites conflicting files. On Mac however, replace deletes the original folder, replacing it with the new folder, therefore every file that isn't a duplicate is lost.
The solution to this is choosing merge. To get the merge option, hold down the option key (alt) when pasting or moving a folder that will conflict with a folder in the destination. This will result in Windows like behavior, only the conflicting files will be overwritten.