Yes, a housing allowance can be amended at any time during the year if a few rules are followed...
1. Be sure the same group (usually the church board) that designated the original housing allowance authorizes the amended housing allowance.
2. Be sure the amendment is in writing, It should be recorded in the minutes of the group that approves it. The minutes should be dated and recorded at or soon after the meeting in which the amendment is approved.
3. Only applies to future payments! This is the most important rule. An amended housing allowance only operates "prospectively". Which simply means that the amended housing allowance takes effect from the date of the approval till the end of the year. Reference: R. Hammar's Church and Clergy Tax Guide