Kristin, there's no way to convey what one doesn't own - you just need to figure out what she owned at the time of the sale. In other words, what needs to be sorted out is if the Duhig rule applies way back in 1987 when your grandmother sold her executive rights to her brother. If it applies, then you are out of luck because the minerals would have been rightfully hers. If it doesn't apply, which it very well may not given the circumstances we have discussed previously, then you have a claim against Encana and/or whoever is being paid the royalties that are owed to your father. You are correct, this is something an attorney will need to determine for you.
As far as the responsible party, the attorney will be your best bet for a definite answer. It seems as though Encana re-ran the title and applied the Duhig rule, so you may have a claim against them if they did so incorrectly, and then changed up their pay decks as a result. I would think Encana is who is liable to reimburse you, if it is them who made the mistake. If they want to recoup the incorrectly paid royalties, then they can file a claim against the owner who has been paid in excess of what he/she should have. Again, this is a general idea of what may be the case, but an attorney is the best place to gain the most accurate information for complicated matters such as this.