The updating of these skins, so they could be distributed, I believe would have to done by the original skinner or their permission to update given to another skinner. 

I did a quick search on WC and only found a screenshot of Metroid and nothing for the other.  The write up on the screenshot shows that it was only released in Europe and was never uploaded to WC.  Doesn't look good for an update. 

From my understanding they would still own the rights to it, so yes it would be a problem.

I honestly don't see that being a problem. They were originally offered for free, we're still offering them for free. Have you seen how many Themes with Nintendo IPs there are here? How long have they been here? Nintendo hasn't taken them down yet. Can you imagine Nintendo going saying, "Well that thing we offered for free 10 years ago and stopped supporting and caring about is being offered for free once again. Lets sue some random guys on the internet." 

And Pixtudio doesn't own the rights for it because they don't own themselves anymore.

Still open guys!

Weboh... if you wish you can wait until Alexandrie and/or treetog see this thread and respond, however they will only inform you that those Windowblinds/skins were a COMMERCIAL enterprise between themselves and Nintendo.

When an artist's [skinner's] work is commissioned the client/customer invariably controls distribution rights - unless agreed otherwise in contract.

The ONLY way an individual could alter/update them would be for him to do that himself...AND NOT publish/distribute the result to a third party by any means...

I contacted Nintendo of Europe for permission, and this is what they said (emphasis mine) : 

Thank you for contacting us to request for permission to use Nintendo properties, unfortunately we are not able to grant such request. As we receive thousands of requests on a daily basis and we do not have sufficient resources to review them all. Therefore, our general policy is to decline requests for permission for the use of Nintendo properties.

However, even though we are not able to grant permission, use of Nintendo's properties without formal permission by Nintendo may still be allowed under the relevant laws of the particular jurisdiction involved. Thus, we encourage you to seek the opinion of your own legal counsel if you have any questions about whether your particular proposed use is permitted without Nintendo's authorization.

Soooo.... is it still a go? And if not, we can at least make themes based off these, right?

Again the answer is 'no'.

As Snowman said...the original authors of the skins will need to be approached first.....as there is no indication [from Nintendo] as to their level of control of the copyright specifically in this instance [because they claim to be too busy to check].  What is needed before they way would be clear is reference to the contract between Pixtudio and Nintendo.

I expect, however that Pixtudio will still retain rights, not withstanding [lack of] response from Nintendo...

So Nintendo owns the rights and they're indifferent. I seriously doubt Nintendo would go after us for this. Can we at least go ahead and see what happens?

No.  You can't go ahead and "see what happens".  Pay attention.

Learn SkinStudio Weboh and make the WB for yourself only. If you try to upload it to any skinning site most likely it will be rejected because of copywright issues. Can you afford the legal hassles?

Such a simple answer that isn't being grasped.  You could only make/modify the skin for yourself with no distribution.

Otherwise....NO.

Weboh you just don't appear to want to accept what is being explained to you, which is your right.   I would of thought that based upon what you were told here you would have come to the conclusion that folks in this community are not willing to go against copyright rules. 

As for myself, I don't really care one way or the other what folks may decide to or not to do, we all have to live with our own decisions. 

Pardon my opinion but what part of NO do you not understand? The N or the O. Just sayin'

Know what.....go ahead and do your thing but bear in mind any difficulties arising from it are on you alone. No one here is willing to go there.