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I'm facing the same problem. I can work around it by making Animal.Id nullable, but that's often not an option. Making it nullable (int? vs int) produces a much more complicated (though valid) SQL.
This manifests after unblocking ExecuteUpdate TPT support (as long as the updates touch only a single table in the hierarchy).
Example test is TPTInheritanceBulkUpdatesSqliteTest.Update_base_property_on_derived_type:
SQL:
Error:
SQLite Error 1: 'no such column: a.Id'.
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