I figured it out shortly after posting. For anyone interested, I loaded all of the dates that are prior to the fiscal year period and assigned the flag. Then I loaded them again but only using the Max value. I joined this back to my original table so only April of the prior period is marked 'Y'.
'Y' AS PriorMonthFlag
WHERE YTD_Flag_Fiscal = 'N' AND Date < Today()
MAX(Date) AS Date
GROUP BY PriorMonthFlag;
Drop Table PriorMonth;