Dictionaries can be confusing.
Most of the definitions I found defined the verb grandfather in terms of ‘exempting’ someone from a regulation or ‘excluding’ someone from liability under a regulation. That's not inaccurate; but it doesn't really describe how the word is actually used.
As the answers at the ELU question Hellion linked point out, the term arose in the post-Reconstruction South, where in many jurisdictions those whose grandfathers had been voters—that is, all local white people—were exempted from the taxes and literacy tests required of others who wished to vote—that is, African Americans, who were recently freed slaves and the children and grandchildren of slaves.
The effect of these laws was that those who were exempt could vote and those who were not exempt could not vote. And that's how ‘grandfathering’ has worked ever since: you are exempted from a regulation which would put you in the unprivileged group, so you are, as a result, grandfathered into the privileged group.
In the case at hand, homeowners who would be ineligible for Federal flood insurance because their homes are in the wrong place on the new maps are grandfathered into eligibility if they had insurance when their homes were in the right place on the old maps.