How do I get my clips back from when Xbox deleted them without giving me any warning...

You don't as the clips and servers are gone

You had ample warning over a year even then they pushed it back 6months and gave instructions to upload to one drive etc

If these are clips you've uploaded long ago, then the online storage may have deleted them itself without warning. This could just be because of low storage issues. I had the same happen to me. Try deleteing some so this doesent happen again, or be sure
to keep a copy on your console from now on. Wish there was a warning though.

I'm having the same problem on the One S. First i thought of giving it some memory space and deleted one clip. The clip would not delete. today it shows up as a thumbnail-less clip that can't be played. I can't upload any videos, the xbox tells me it's uploading
and it tells me the clip has been uploaded to live, but when i check theres nothing there. On the mobile App I get the notification that a clip has been uploaded and I can view the clip on my phone, but if I try to share or save the clip it says a problem
occurred. As soon as I leave the clip page, it disappears from the captures tab on the app. The clip I deleted on my xbox doesn't show up on my Mobile App, thats a good thing.

I have had multiple game clips deleted or vanished from my xbox local drive as well as on xbox live without me deleting or doing anything. It seems some clips stay forever and a lot eventually go away. Is this supposed to happen and is there any
way I can retrieve those clips or are they gone forever?

you are not the first one today to post this it may be a bug

Unsaved clips are now auto deleted. You can click on save on the clips you want to prevent them for being deleted. Unfortunately theres ni way to get deleted clips back. Give a try at xboxclips.com by searching for your gamertag.