In the Actions menu, the Merge 
command performs a merge of the selected files and folders.
If a folder is selected, only its filtered contents will be merged (same as if the folder was expanded and all visible contents selected). However, if an open folder is selected and any of its children are selected as well, then the folder's selection is ignored and only the selected children will be merged.
By default, a confirmation dialog appears before the merge. To skip the confirmation, choose Tools | Options 
(Beyond Compare | Settings on macOS), switch to the File Operations page, and clear the Confirm file merge checkbox.
