Integrity service reports file as having obsolete checksum on two pillars, when the file is actually missing on the two pillars

The service have once seen the file (it has size and a creation timestamp), but have no checksum for the two pillars. For the two pillars the service db have a checksum timestamp set to epoc, even as it has no checksum (it's null).
1) The files are not marked as missing (i.e. the update step of fileIDs is broken)
2) The files are not marked as having a missing checksum
3) The files are marked as having a too old checksum, which is wrong, they have none.