In Google Drive you can download a non-native Google file (e.g. MS Office, PDFs, etc) to edit locally, and then re-upload the new version. In the past, this would result in duplicate files (the original and the new one), and finding the latest version was challenging. This is why Google introduced a change in Drive to deduplicate files which were uploaded in this way.
With this new feature, files that have the same filename as an existing file, will be deduplicated, and the old file will be placed in the revision history. This is so that if any mistakes are made, the previous version can be restored. Uploaded folders are merged with folders of the same name.
To prevent the files from being deduplicated, click Keep as separate file once it’s uploaded.