If you can statically define the batch tools task take a look to the Extra>TaskAutomationFolders tool.
With this tool you can configure a sequence of tasks to be executed when, in the monitored folder, PDF files are created/changed.
Another option is to use a command line tool, for example
PDF-ShellTools command line interface, and create a DOS batch, or Windows Script, file to perform these custom tasks you often execute. In next PDFE version there is the possibility to call external application/scripts from the interface itself, passing selected grid files as parameters.