We narrowed down this issue.
We extracted one of the .biar files which contains .lov files. Each object in a universe is associated with a .lov file.
According to SAP, .biar files exported with the "Import Wizard" on Business Objects 3.1, have a limit of 1000 .lov objects. So in our case, the ITSM universe had more than or equal to 1000 .lov objects, which made the file corrupt.
The issue does not occur if migrating "Live to Live".
The 999 object limit has been removed as of Fix Pack 4.4 for BusinessObjects Enterprise 3.1, according to SAP.