lets say that the 'Subject' for one of the files is quite many, under the Filename, PDFEManual the subject is (hypothetical!)
Subject: Algebra/Geometry/Word Problems/ Verbal/Math/English etc
and to make changes to 3000 other Filename Subjects, creating interface similar to Itunes edit option will be helpful for user. This way, once I filter down the files to edited, then click on their boxes, then open an edit page similar to itunes' then I can just click on next while having the ability to see the name of the file that is been changed.
I'm not a iTunes user so I'm really not getting the idea here, but I'm going to check.
Why can't I just press 'Enter/Return' on my keyboard to ensure that the changes made are made? Instead of having to use the mouse to click on 'Save' over and over again?
On that PDFInfo tabsheet view, you just need to change to another file, clicking another grid row (or using the CTRL+UP, or CTRL+DOWN keyboard shortcuts to move to previous or next file), to apply, automatically, any InfoEdit changes to the PDF file and PDFE database. That save button, that can be triggered using the CTRL+S shortcut, exist mainly to show user that changes exist, and to apply changes if user don't want to change to another file.
Also, on these multi-InfoEdit sessions, where we are going to edit metadata on many files, it's much more useful the Edit>QuickInfoEdit(F4) mode. On that mode you see the file content itself, not just the filename, have a previous and next buttons (but the respective keyboard shortcuts are much more handy), and the help of the QuickInfoEdit Assistants.
These assistants are used while copying text from the PDF content (or the copy of raw text image that can be converted back to text with the Quick Image OCR assistant), facilitating the process to send that copied text directly to a metadata field.
On this mode you don't need also to click the save button to apply changes, you just need to move to the next, or previous, file.
Why isn't there an 'undo' option? With the batch tools, mistakes could be made that'd affect thousands of files...and trying to correct each file, one by one is extremely time consuming.
Yes, batch tools are "dangerous"

, but implementing a undo option is not a easy subject for some of the functionalities. Already in the TODO list but, for now, just a thing to think about.
Referring back to Duplicates, is it possible to click on a file, right click, then click on a duplicate option that finds other files with the same name and so on?
If eventually the find duplicates tool is implemented, not a big problem to interface it from the right click menu, but I don't see it as a so important feature to interface it from that menu!
Lastly, for now, 
Keep them coming

Is it possible for the name of the files clicked on to be edited in 'Batch tool - info edit', show under file names? This way, mistakes can be caught on much faster.
"Under file names"

Show files to process in a file list of the tool dialog itself, as with the Tools>Stamp/Watermark tool?