You could use the Remote file search feature under the Tools on the main menu to search for *.sql files and then queue the results, this will add the file selection to the queue with all of the files being queued to the same target location without creating any folders.
You could then save this queue for later re-use but it would need to be manually updated to include any newly created sql files.
Alternatively you could transfer the files with the folder structure and then find another program to consolidate all of the files into a single folder.
I am not sure if either of these solutions are ideal, but if there is a slight chance of multiple sql files with the same filename then a single folder might not be practical.
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