So, PANDA doesn't have any direct support for something like that.
Besides lines that are exact duplicates, are there lines where some cells are identifiers (a person's name, or a unique ID) and other cells are updated values (like if the person got a raise)?
If the only issue is pure duplicate lines, I'd probably write a simple script that reads the old file and the new file and spits out only unique lines. Not the most user friendly, of course, but…
If you want to update some rows as well as insert others, then there's really probably nothing easier than deleting the dataset.
I could see having a PANDA feature which is "replace data" alongside the "upload more data"; we'd want to think it through a little, but it seems straightforward logically. It would save you from re-entering the metadata, and it could also keep a reference to earlier files which could be downloaded but which wouldn't be in search results.
Technically we could probably do something like "merge data" to save you from writing the script mentioned above but I feel like that starts to run the risk of some weird edge cases.
Joe