The WinSxS folder is critical to Windows and removing it can cause issues. If there's one in the %SYSTEMROOT% folder on the C drive, then it's possible that the other one is from a previous installation or updates as stated. The MS article here states that Disk Cleanup can potentially clear out some of the files in there. This link shows that it should not be in folders other than where Windows itself is installed at:
So obviously you cannot delete this directory or move it elsewhere. Nor is it advisable to delete anything here, as such a step could probably make your applications un-workable or even break your system! If you have many applications installed, you can expect to have a jumbo sized winsxs folder. This WinSxs folder cannot reside on any other volume than the system volume. This is because of the NTFS hard links. If you try to move the folder, it may result in Windows updates, service packs, features, etc, not installing correctly.
If the folder is not on the same drive as Windows, then it should be safe to remove, but back everything up first, just in case.
On a side note, if you have Windows 8.1 or later there's a utility that you can use that will attempt to reduce the size of the winsxs folder. It can be found here.