You can create custom "Selective Transfer Lists"
Tools > Selective Transfer > Edit
A selective transfer list lets you define a list of files that you can either include or exclude from being transferred. To simply transfer say all *.html files is really simple to do.
Here is an example video that shows you the steps you need to take to set it up.
http://www.trvx.com/demo/1/
Once you created the selective transfer list you just need to make sure it's activate and then queue up the folders and transfer away
FlashFXP will always default to the default list on startup.
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