Here is the scenario in which the plugin fails:
wiki1: Upload media file test.txt in the root namespace
wiki2: sync with wiki1 -> copy the test.txt file from wiki1 to wiki2
wiki1: Now download the test.txt file from wiki1. Add a few lines, save it and upload it again by overwriting the original test.txt file on wiki1
wiki2: sync with wiki1 -> the plugin does not detect the changes