When you want FlowJo to repeat a layout you have made, substituting other samples for the current ones, there are several options available. See Batching (overview) Iteration (details)
FlowJo can organize a batch by sample, by
stain panel, or by keyword. (Complex batches can be organized by a
sequence of these parameters.) Set these preferences with the
drop-down menus at the top of the Layout Editor.
If batching is set to a particular Sample name, and a different sample is dragged in to the Layout Editor, FlowJo needs to know how you want to handle this "Iteration Mismatch."
Go to Edit > Preferences and click the Layouts
button. 
Under Drag Mismatch Policy you have the following options:
If batching is set to a sample name, and a different sample is dragged in to the Layout Editor, this setting tells FlowJo to:
- Turn Iteration off
- Change the dragged sample to the one currently specified in the Layout
- Change the Layout setting to match the new sample
- Ask the user to choose
