The changes made with /fill command are not saved when you exit and re-enter the End (or exit and reload the world).

The blocks replaced with air can come back again when you reload or re-enter the end.

Steps to Reproduce:

• Enter the end
• Move away from the main island
• Use the fill command to place a layer of blocks /fill ~ ~ ~ ~40 ~ ~40 stone
• Exit and re-enter the end
• Use another fill command to replace a portion of the stone with air
• Exit and re-enter the end
• Notice that the stone may have partially come back
  (May take a few attempts, though it was pretty consistent)

See attached screenshots which show what is happening.