This might help. I ran a duplicate check program on the complete extracted folders. In the rar are the results of the dupe search and what is left over in the folder. What is somewhat odd is some of the files are the same size, same date but are in fact not the same crc value, therefore not the same. By downloading all the mods and UBR we are overwriting files which are not the same.
BTW The program I ran on the folders could care less about name,date or anything except the crc value.
Note if you care to look at them the files ending in Dupe Results.txt are the files deleted as duplicates even though the filenames may not be the same.
The files ending with List.txt are what is left over after the dupe removal
Duplicate File List UBR vs Mods.rar
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