Good news: D1 is on the PCB and has a footprint (0402 TVS). The “Missing Footprints” DRC is clear. You’re likely just not seeing it on canvas.
What Flux docs say about finding it
“Navigation
Click on any category to expand or collapse it
Use the search field at the top to find specific objects by name
Right-click on the tree background for additional view options
Selection
Click on any object in the tree to select it in the PCB editor
Hold Shift to select multiple consecutive objects
Hold Ctrl (or Cmd on Mac) to select multiple non-consecutive objects
Right-click on an object for a context menu of actions
Visibility Control
Click the eye icon next to any object to toggle its visibility
Use the visibility controls at the top of the tree to show/hide entire categories
Right-click and select ‘Hide Others’ to focus on specific elements”
Source
Do this
Open the Objects list and type “D1” in the search field; click it to select. The footprint will highlight on canvas. If it’s still not visible, use the eye icon to ensure it isn’t hidden.
Current DRC summary
Airwires: EN, IO0, RXD0, TXD0 between U1 and test pads TP1/TP2/TP3/TP4. No “Missing Footprints” errors.
When you’ve located D1, tell me and I’ll guide you to place it close to J2 and clear the airwires next.