Why is there a winsxs folder on D: drive and can I safely remove it?

Question

I recently purchased a refurbished laptop with mSATA boot drive (C:) and a spinner disk (D:), with Windows 7 Ultimate + SP1 pre-installed. I had intended to have the entire system on C:, leaving D: free for me to do whatever I want, including changing the partitioning, reformatting the whole thing, or replacing it.

What I found is that there appear to be some system folders on the D: drive, and Windows won't let me shrink the D: partition beyond about half the size of the disk, stating that there are files that have fixed locations on the disk and cannot be moved.

In particular, there are winsxs folders on both C: and D:, with some subfolders/files on C:, some on D:, some the same on both, some on both but different. If I try to compare a sampling of files with BeyondCompare, I find that it is able to open all of the files that I tried that are on C:, and none of the ones I tried that are on D:. There are many, many files in both locations.

The vendor says these files are from installing Windows updates, and that I can just delete them and reformat the disk if I like. I'd like to confirm if that is a safe thing to do, or if I'm going to have problems with System Restore or later Windows updates or something annoying like that.

I've also been researching moving that folder, but most sites, even the ones that give instructions for doing so using junctions, really recommend against it.

I'm considering just creating a System Restore disk and System Image Backup and wiping everything out and starting over from that.

Answer 1

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.