If a report based on a Custom Report Type does not contain all of the expected fields to add, you must edit the layout of the report type in question.
For example, an 'Accounts with Opportunities' report type is missing fields from the 'Select Columns' step of the Report Builder.
The following steps help you add missing fields to your report:
Note: If previewing the layout, all fields and objects are displayed, including fields and objects that you don't have permission to access. You can access only the data that is stored in the fields or objects that you have permission to access.
When you go back to the report, you will find that the fields are now available to be added to the report.
Create a Custom Report Type
For additional helpful tips, see the Salesforce Help page - Design the Field Layout for Reports Created From Your Custom Report
Idea Exchange - Let us customize which fields appear on standard report types
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