Currently the built-in 'Swap...' button in flash cannot be used when multiple items are selected on the stage- even if they are all instances of the same symbol. Use the 'Swap All' command to get around this limitiation and replace multiple selected instances with a selected item from the library.
To use the Swap All command:
1. Select the items on the stage you would like to swap with an item from the library.
2. Select the item from the library you would like to 'swap in'.
3. Go to Commands > Swap All and click OK when the dialog appears.