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Emptying or covering holy water fonts during Lent is a modern innovation not found in the Church’s directives. Water is always kept in the holy water fonts until after Mass on Holy Thursday, when they are emptied of holy water and later refilled with the water blessed at the Easter Vigil (Paschales Solemnitatis 97).
Lent is a time when we need the spiritual benefits of holy water. Holy water is a protection from evil, a reminder of our baptism and of our commitment to live a Christ-centered life. Empty holy water fonts during Lent only deprive the faithful of spiritual benefits that are theirs by right.
The General Instruction on the Roman Missal requires a crucifix to be present during the celebration of the Mass. It may be possible to get away with replacing the main sanctuary crucifix with a cross if there is another crucifix present at least during the Mass (e.g., if an altar server or crucifer bears a crucifix into the sanctuary during the entrance). The covering of crosses is permitted during the last two weeks of Lent (approved by USCCB and Holy See, effective April 2002). The rubrics for the fifth Sunday of Lent state:
In the dioceses of the United States of America, crosses in the church may be covered from the conclusion of the Mass for Saturday of the fourth week of Lent until the end of the celebration of the Lord’s Passion on Good Friday. Images in the church may be covered from the conclusion of the Mass for Saturday of the Fourth Week of Lent until the beginning of the Easter Vigil.