Currently, within this plugin, you can provide a pattern to exclude files in which you do not want to transfer. Also within this plugin, there is an option to "Clean remote" which enables you to wipe out the remote directory before transferring files.
The ask is to be able to provide an exclude pattern for the files which are being wiped from the clean remote option. So there would be two exclude patterns within the configuration. One to exclude files to transfer, and one to exclude files to delete when remote clean is enabled.