I'm not quite sure the best way to describe this.
Thankfully it looks like it did not affect the actual save, just how it's loaded.

There's a number of things I'm seeing.

This is an example of a saved set using 3.5

This is that same set in the listing and when I click in 3.6.3

And I'm getting all sorts of wrong items showing on both the preview and when I click it. It's not just ones with normal/heroic/mythic versions of the same items.

Here's another comparison that also shows the difference on multiple saved sets. (The previews match what gets applied, so it's not just a display glitch)

3.5

3.6.4

I've not saved anything since this update, but I' have swapped back and forth between versions. I can't say what would happened if I were to save anything, but as it currently looks, this is only affecting the load of the sets and did not affect anything stored in the saved variables files.