This notification indicates that there are files with the same file name, but different case. For example there may be a file named ‘Test.txt’ and another one named ‘test.txt‘.
While duplicate filenames may be accepted on some operating systems, it is not on others. Since the client synchronizes data from various devices, it may become an issue if the files are transferred to a device which can’t handle duplicate filenames.
If this notification appears in the client, you simply have to rename the files by selecting new, unique names for each of them.