For example, power symbols do not have footprints assigned. Schematic symbols can also be used as placeholders for other stuff. Schematic symbols have an Exclude from Board ckeckbox and there are are variants when not all components are placed on the PCB (even though they have footprints on the PCB).
If you turn on Replace footprints with those specified in the schematic during Update PCB from Schematic [F8] then Schematic symbols without assigned footprint links get flagged:
Sure, there are lots of symbols without footprints. I was trying to emphasize that in the relevant case here, where the symbol in question had a footprint assigned and no longer does, there should be an error upon updating the PCB with “Replace footprints” checked. (As you show in the screenshot)
My understanding was that there wasn’t an error being shown, even though leoheck mentions using the 3rd option (“Replace footprints”) in an earlier post. That would seem to be an issue and worth following up on with the project files (or a stripped down version of the project).
In a future version of KiCad, this checkbox will be UNCHECKED by default because of the confusion it causes in instances such as yours and especially with Geographic Reannotation. As you have found, it basically resets your PCB layout. This operation is something that users should RARELY need to do.
