This requires FlashFXP v4.1 build 1902 or newer.
With the latest beta release this can be done with additional configuration of the queued delete.
Load the queue file, then from within the queue window
right-click on the folder to be deleted and select edit. From the
edit dialog uncheck
Include sub-folders click
OK and then save your modified queue file.
When the option
include sub-folders is unchecked the folders within will not be deleted and neither will the folder, only the files will be deleted.
Download FlashFXP 4.1 beta
Another new feature in the 4.1 beta is the ability to define file masks for folder delete operations, so you could then enter a file mask of
SmartExport_DW*.zip and only the matching files within the folder would be deleted.