Two shulker boxes disappeared out of my ender chest.

I was in the nether.  Just finished raiding a bastion.  Filled two shulker boxes, placed them in an ender chest.  Traveled back to my portal, went through the portal.  On the other side of the portal, I was glitched inside of blocks at the corner of my portal.  I broke two blocks and back to normal portal height.  Then went into Minecraft house, where nearly half of my double chests were glitched to single chests.  I tried to open one, game shut down with an error message.  Error message: game closed because of error.  Closed application, reopened it and opened my world.  When the program opened, I was in the nether near the bastion where I placed my shulkers in my ender chest. I went back to my Minecraft house and back to the bastion a few times. The shulkers where nowhere to be found.  One of the next couple of times I went through the portal, the same glitch happened.  This time I didn't lose anything though, I did get the same error message.