Variable assignments not sticking, after publishing

In a recent audit, I made some corrections in our variables library. After which, I ensured all updates were applied, then published the library. 

I first updated all pages in our main component library. I then audited/updated ALL variables that required manually change (because there was a net new variable that needed to be attached to a component). 

After which I ensured all updates were clear, and then published our main component library. I see this in history log as well. However, when I look at the variables applied/linked to the components, they still show the old/deprecated/deleted variables, that I either updated, and/or manually applied. Again, I see the correct changes applied. And I even see the save point in the history. 

However, now days/weeks later, the components (updates, or manually linked) are showing the old variables still linked. And if I go back to the save point, it also shows the incorrect/old/deprecated/deleted variables still applied.