/kill @e[type=Item]

/testfor @e[type=Item,x=40,y=1,z=40,dx=40,dy=27,dz=80] {Item:{id:"minecraft:banner",Damage:4s}}

/scoreboard objectives add ItemToRemove dummy

/scoreboard players set @e[type=Item] ItemToRemove 1

/scoreboard players set @e[type=Item,x=40,y=1,z=40,dx=40,dy=27,dz=80] ItemToRemove 0 {Item:{id:"minecraft:banner",Damage:4s}}

/kill @e[score_ItemToRemove_min=1]

/kill @e[type=item,nbt=!{Item:{id:"minecraft:banner"}}]

/scoreboard players tag @e[type=Item,tag=!isFlag] add isFlag {Item:{id:"minecraft:banner",Damage:4s}}
/kill @e[type=Item,tag=!isFlag]

/kill @e[type=Item,name=!Flag]

/kill @e[type=Item]