The dispute was over the ownership of two buildings and land in Lethbridge.
Henry had argued that under the church's canon law, the Catholic Charities Clothes Bank of Lethbridge falls under his authority.
Earlier this year, a judge disagreed and ordered the Calgary Diocese to transfer the titles of the properties to the Lethbridge charity.
The Alberta Court of Appeal has overturned that ruling, citing legal and factual errors.
The appeal judgment says that while canon law is not a factor in the case, the Calgary Catholic Diocese is the legal owner of the properties.