You can customize your PBS, but there are several things to consider first, as it will have an impact on other areas of SDx:
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All forms with references to the PBS will need to be customized accordingly.
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All Data Validator (including submittals) will need customization (or even input format changes) accordingly.
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For each different branch in your custom PBS, you will need to setup a new relationship definition and assign access to it accordingly.
For information about the rules to modify the data model, see Configure the data model.