Sort out the media/clip relationship between master clips and subclips
Subclips should be traceable back to Masterclips. If you can track duplicate clips across projects in Productions, then surely it is possible to create a link between the source master clip and subclips. It seems that forums and even Adobe staff are recommending against using subclips and nodes does seem to be using them for this terrible reason. While on this subject the behaviour of subclips and the Project Manager is a nightmare - every subclip (or sequence clip) in a project results in a another copy of the underlying media. So single promo made out of 100 clips from the same taste clip results in 100 copies of the same media if sent to the Project Manager.
Marion Autokroma commented
Hi Alex, this is a known bug of the actual Project Manager.
As a workaround, you can delete copies of your original files and keep only one, then relinked all subclip project items to the only one left.
But this solution can be really long in your case with 100 clips from the same file.
An alternative solution is to use a plugin called PlumePack (https://www.autokroma.com/PlumePack), it works almost the same than the project manager but with less bugs like this one and with also a a Trimming feature with handles! This feature will remove the unused data of your media without re-encoding the file compared to Project Manager: your files keep their codec and exact quality.
This should solve your issue with subclip duplicated.