Many thanks for answer.
drush upe is a method linked to Entity Update.
I also tested with Devel Entity Update (drush entup) and got the same result.
I think the problem comes from Views Reference, as the three fields I can't update are of this type. I'm also looking at Views Reference, because the 3 fields causing the problem are of views reference type. When I try to modify these fields, and I want, for example, to set a default parameter (an Entity Reference view and display), I get the following error when I save:
AH01071: Got error ‘PHP message: Uncaught PHP Exception TypeError: ’array_intersect_key(): Argument #1 ($array) must be of type array, null given‘ at /core/lib/Drupal/Core/Entity/Sql/SqlContentEntityStorageSchema.php line 2479’, referer: /admin/structure/types/manage/projets_programmes_de_recherche/fields/node.projets_programmes_de_recherche.field_pub_anr.
When I specify a different display mode, I get the same problem...