The law isn't retrospective, though. It would only be retrospective if it affected the Relief you could claim before it came into effect, which it doesn't. What has changed is the rules which affect your entitlement to claim Relief from that date forward.
Your entitlement to Relief depends on circumstances which predate the change, that is true (i.e. the fact that it was empty), but this does not make the law retrospective.
The new rules say that you can only claim Empty Property Relief for the first six months a property is empty. If those first six months were before 1st April, there is therefore no further entitlement to Relief.
Sorry it's not the answer you were looking for, but as I see it, they are interpreting the rules correctly in this instance.