Generally speaking, if you have customized an out of the box component, then it will be skipped during the upgrade. The number of skipped changes after an upgrade may differ from prod to sub-prod / sub-prod to sub-prod. This will be due to that fact that the data in both instances are not completely in sync.
This could be due to two reasons:
- A full clone was not completed prior to the upgrade
- Changes were made within the instance after the clone and before the upgrade
1. One reason you could see a large number difference between instances after an upgrade is because a full clone was not performed prior to the upgrade.
A full clone (where nothing is excluded) is required to show best case for an upgrade. Review the clone history and check if the 'Exclude tables specified in Exclusion List', 'Exclude audit and log data' and 'Exclude large attachment data' options were all checked, these need to be unchecked during a full clone. If they have not been fully cloned, you can never be certain that one instance is an accurate representation of another, and you may see discrepancies in the 'Skipped Changes' numbers.
In the case of looking at two sub-production with this mismatch in numbers, ensure if the same backup of prod was re-used or if a new backup was used for each clone.
2. Another reason the numbers may slightly differ is due to the number of updates that are made to the instance after the clone was done and before the relative upgrades. May be worth checking to see if there are any sys_update_xml records created after the clone and before the upgrade took place.
Over the course of the period between clone and upgrade, development could be taking place and changes could have been moved through these instances, and it's almost impossible for the two to remain perfectly in-sync. All of this has an impact on the Customizations Unchanged and Skipped Changes to Review lists. The main thing to pay attention to here is that the Upgrade Details list shows the exact same number between the two instances. This is a clear indicator that all the same updates were applied to the two instances.