In new versions, an Indicator or Investment Priority cannot be removed and is checked by a validation rule. If you no longer wants to use an Indicator/Investment Priority you should set the values to 0 in the different tables associated with that Indicator/Investment Priority.
For an Investment Priority, even when the values are set to 0 it will stay in Table 1. In the Justification you can explain that it is not used anymore as of that new version. Table 3 and 5 should be set to 0 and all text under that Investment Priority can be modified to indicate it is not used anymore.