You have changed/added/removed code or components that was in Workflow projects, such as SD.IncidentManagement or SD.RoutingRules, and then republished these, or, added entirely new projects that were never in the out of box product. These are referred to as customizations. You want to know if these customizations are kept when upgrading or reinstalling ServiceDesk.
Customizations are not necessarily kept when upgrading or reinstalling ServiceDesk.
Upgrading (such as from MR1 to MR2)
During an Upgrade Install, the user is prompted to select which projects to overwrite, which will result in the customized older projects being overwritten with their new uncustomized versions. When performing an upgrade, the new project versions are crucial for ServiceDesk to continue working successfully. Warning: If the user unselects which projects are upgraded (in order to keep older code customizations), or later restores older versions over newer versions, this will result in possible loss of functionality and/or hotfixes not being applied. This is not recommended or supported.
The only supported method of migrating old customizations from one version of ServiceDesk to another is by manually re-implementing these into their new project versions. For example, if a customization was made to the old version of SD.IncidentManagement, the same customization would have to also be manually made to the new version of SD.IncidentManagement. This is unfortunately unavoidable due to how Workflow projects work in conjunction with ServiceDesk.
This works in the same was as upgrading. However, specific projects can be unselected to be reinstalled in order to retain customizations easier. If the reason for reinstalling ServiceDesk is to correct issues, however, it may be necessary to revert the customized projects back to their original versions, at the least for testing.
ServiceDesk 7.0 MR2 Release Notes
After upgrading ServiceDesk, certain areas no longer work as they used to
How to restore a ServiceDesk Workflow project to its out of box version after it has been customized
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