Comment # 13 on bug 1078487 from Wolfgang Bauer

(In reply to Karl Cheng from comment #11)
> As mentioned in comment 9, kde#389991 provides instructions to manually fix
> this, which resolved the issue in my case.

Should be fixed in Plasma 5.12.2 then, which was released yesterday (it's not
in the repos yet though).

> However, I'm not sure whether this requires manual intervention or if it can
> be handled by a package update.

The fix that will be in 5.12.2 should not require manual intervention AIUI.
After the update, the shortcuts should get migrated again, and this time the
migration should work fine.