During testing of a hopper clock, blocks disappeared while moving into the locked hopper.

While the clock is running (Switch in OFF position), the stacks of blocks can be moved using Shift + Left-Click.

When the clock is switched off (Switch in ON position)

• The blocks are still transferring between the hoppers. first moving to the left and then to the right.
• Grab the stacks of blocks (Shift + Left-Click) from the unlocked hopper into player inventory.
• Place the stacks from the player inventory into the locked hopper (Shift + Left-Click)
• Not all blocks will transfer (See TheIssue video).

Attachments:

• Contraption: the hopper clock being tested.  Contraption is built along the X-axis. image taken facing the -Z direction.
• Chunkposition: contraption is on the edge of a chunk but does not cross it.  
• TheIssue: video showing transfer of stacks and disappearing blocks.