Changes to the church and religion in the period 1540 -1629?

You need to get specific about which church and what location. For most of that period, in Europe, every chapel was an independent religion. Roman Catholic became dominant because thieves and murderers overran the new world and sent large amounts of gold to their church and the Spanish government. The Spanish crown was not as wise as the Catholic church, so all that gold was in other countries within a century.