TreePadGen 1.1 is now available on my site. I've added TreePadAdd.exe to append new entries to the TreePad file generated with TreePadGen. Also the dummy comment for each node is optional via .ini file setting.
Example usage of TreePadAdd would be several new downloads in your download folder. Run TreePadAdd and manipulate the FileOpen Dlg so that newest files are at the top. Select the new files. They will be appended to the TreePad file for that folder.
edit: Important note.. TreePadAdd just assumes the target .hjt file has been created with TreePadGen. Run TreePadGen to create the initial .hjt file for the folder so that the folder name will be the root node. As I update I'll probably end up merging the programs or adding some code to check for this condition and provide an option to generate the TreePad file etc.. Most likely I'll just call TreePadGen from TreePadAdd if the target .hjt file doesn't exist. I'll work on it.

Note: I haven't seen any easy method for merging TreePad files with comments onto an existing TreePad file so that you could import a tree and have the comments overwrite the dummy comments. This method at least makes it a bit simpler to add new files as your download folder grows. Maybe some multiple clipboard utility would make it a bit easier to add the file comments.. but for the time being this approach would seem to work on any Windows XP or later independent of 32 or 64 "bitness."
(The modification has been submitted to Softpedia. Typically it will update in one or two days.)