With the recent update for ps4 that brought us onto the bedrock version of the game, I decided to update the world that I had. At that time, I was unaware that there was the potential to switch back to the old version, so I simply deleted the old worlds. After playing on the updated world for a while, I was in need of some of my items and went looking for them. It was at this moment I realized that every single one of my default colored shulker boxes had been deleted from the chests they were in. The dyed shulker boxes were perfectly fine and in order, it was only the boxes that were undyed. I then went over to my creative test world to see if the same thing happened over there, conveniently I had been working with shulker boxes there as well, and once again, only the non-dyed boxes were deleted. Since I noticed this after I thought I was in the clear, there is no way of getting them back, and know it is impossible. I just hope that nobody else makes the same mistake.

tl;dr: Non-dyed shulker boxes got deleted as I updated my worlds