Replace Node Dialog
When you drag a node (or a tree) onto another sample which has a node with the same name, then you are presented with the dialog shown below. (Note that if you are dragging a node with its parents (holding the control key down during the drag), then it is the name of the top-level parent which is compared to nodes underneath the destination node.) Choose one of the four options by clicking on the buttons.
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The Cancel button will discontinue any more copying of analyses to the destination. The Rename option will cause the nodes you are dragging to be added to the destination with its name modified by a version tag (e.g., "-2" is added to the name). Retain tells FlowJo that you only wish nodes that you are dragging to be added to the existing tree if they do not already exist--i.e., the existing gates in the destination sample will be unaltered. Replace tells FlowJo to replace the gates (which have the same names as the gates you are copying) with the versions of the gates that you are dragging.
These options are more fully described in the page on node replacement.