In the compare report dialog window there exist a checkbox option "Update Item Status/Child Definitions" (highlighted in the below screenshot) which is the cause of this behavior. If this checkbox is selected and if the record is of same version in both source and target databases the system removes the field's from the upgrade project definition.
Below is the notes from PeopleBook after this checkbox option:
Deselect the Update Project Item and Child Definitions option to preserve the status of the items in your upgrade project and the child definitions when running a compare. Child definitions apply only to records and fields in which fields are the child definitions of the record, and field labels are
the child definitions of record fields.
When running a compare report, the system compares the definitions in an another database or file to the database to which you are currently signed on. Based on the compare results, the system updates the status of the project items in your upgrade project in the definition window. For example, after running the compare, the system inserts the status of the Source and Target (Absent, Changed, Unchanged, and so on), the Action to take (None, Copy, CopyProp, and so on).
Regarding child definitions with the case of records, if a record is the same version in both places, the system removes the fields. With the case of fields, if a field is the same version in both places the system removes the field labels from the upgrade project definition.
When a child item is found to be different between the two places, then that item is inserted into the project so the child item can then be copied as a unique item. When this option is deselected, no child items are deleted nor inserted into the project.
In some cases, as in when you want to compare the same upgrade project to multiple sources, for example a demo database, a production database, and a project file, you may decide to deselect this option so that the source upgrade project remains unchanged. When deselected, the project item
status and child definitions information only appears in the generated compare report, not online in the PeopleSoft Application Designer project definition.
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