How can I identify my Rips which have been duplicated by ember

OK So I have spent hours ripping my box sets of Battleship Galactica. I only have seasons 1-3 but not 4 yet.
I used Handbrake to rip the DVDs into various Season folders before moving them to my Media PC. I used the queue system so it ripped the DVD contents into episodes which I named in advance. I named them according to the standard format e.g. For Season One S01E01, S01E02 For Season Two S02E01, S02E02 etc etc. (However I incorrectly named the season folders Season 1 Season 2 instead of Season 01 Season 02.)
I then pointed Ember at the TV shows and allowed it to scrape the fan art and data etc.
Now when I look at the PC I have new folders and files left in the old folders e.g.
Season 01
Season 1
Season 02
Season 2
The majority of files have been moved into the new Season 01 and Season 02 folders but there are still some left in the old folders that appear to be duplicates but haven’t been scraped so still have the file names Battlestar Galactica S01E01, Battlestar Galactica S01E04 etc. I therefore cannot ascertain which episodes these are and which are duplicates without watching every clip. Episode 04 in Season 02 is different to episode 04 in folder Season 2

1) Firstly how does ember rename files. Does it copy them into a new directory and then delete the old directory?
2) How does it deal with duplicates e.g. incorrectly named files?
3) Does Ember have a Log which shows which files have been renamed?

I have searched for software that can scan the video files (all mp4) to find duplicates but only the paid versions work and have identified numerous duplicate files but won’t tell me which ones they are unless I purchase. Is there another way I can compare the files perhaps frame by frame?
The only info in the metadata of each file is the creation date and time. If I could sort by created date/time in some program that ignored directories that might help
I am starting to lose hope and quickly coming to the conclusion it would be quicker to rip the whole lot again although most took all night to do.Sad
Does anyone have any ideas?
Fozzie