That’s right, it’s actually my cached footprints, perhaps from 4.0.5 or 6. I reckon pcb-new could do with a menu option that refreshes all the utilized footprints with the one it’s cached from. Or a table could come up with those used and the user selects which ones to refresh.
We added the reference on fab after KLC version 2.1. (Beginning of 2017, after 4.0.5 but i think before 4.0.6)
For the MSOP package the reference was added on 11.April 2017. (This was after the v4.0.6 release)