If you click the accounts button on your report table you will see the different reports names (for example Setup, Single Period Report, etc), did you name your new report to a different name?
Select the Accounts button and select Setup, the three columns you had removed should appear. The three columns are missing for that report you had created.
To restore your columns
I suggest that your perform a Workstation backup (File > Backup) on your workstation table and then on the report that you are missing the 3 columns, right mouse click on the report title bar and select Window > Default Setup and click OK to restore the Reports to the factory defaults.
I hope this helps,
Regards to All