I am sorry if this is a duplicate and also when this works as intended, but I thought the blockdata has the funktion to change partwise NBT data of blocks
So when you use the blockdata command to change for example the name, the other NBT tags like "lock" don't get overwritten, so I guess items also shouldn't overwrite everything

How to repdroduce:

1. Place a dispenser and fill it with some items
2. Stand on top of the dispenser and perfrom this command:

   /blockdata ~ ~-1 ~ {Items:[0:{id:stone,Count:1,Slot:4,Damage:0}]}
   

   You will see, that the dispenser only contains the stone anymore, but the other items are gone

This should instead be made by this command:

/blockdata ~ ~-1 ~ {Items:[0:{id:stone,Count:1,Slot:4,Damage:0},1:{Slot:0},2:{Slot:1},3:{Slot:2},4:{Slot:3},5:{Slot:5},6:{Slot:7},7:{Slot:8}]}