Product:
Cognos Analytics 12.1.1
Microsoft Windows 2019 server
Issue:
During over-the-top upgrade of CA, you get a error that folders in use c:\program files\ibm\cognos\analytics\cgi-bin

Solution:
Stop the IBM Cognos service, and also stop the World Wide Web Publishing Service.
Try then to run the installation again.
More information:
Before upgrade, backup the content store database, and export the content to a zip archive from Cognos.
Export the Cognos Configuration to a xml file.
During installation, the [Cognos Install]\deployment and the [Cognos Install]\data\search folders will be moved twice, which can cause the installer to appear as though it has stopped working. As these folders are often very large, it is advisable to move them to a location outside the Cognos Analytics installation folder prior to applying the update, then move them back after the update has completed, prior to restarting Cognos Analytics.
Upgrade steps on Windows:
1. Stop the Cognos Analytics Service and close down Cognos Configuration. If you have installed an optional Gateway, please stop the Apache or IIS webserver services.
2. Launch the downloaded installation file and follow the wizard.
3. Choose your Language and click Next.
4. Choose What you want to install – for an upgrade this will be IBM Cognos Analytics click Next.
5. Choose to Accept the license and click Next.
6. Choose the location. This must be the location of your Cognos Analytics instance that you would like to upgrade and also the shortcut folder name. Click Next.
7. Click Yes to confirm you are Installing in the same location and are overwriting a previous installation.
8. Click Install at the summary screen.
9. When complete click Done to complete the upgrade.
10. Open Cognos Configuration – you will be prompted that older versions of Configuration files were found and configuration files have been upgrade to the latest version. click OK and Save your configuration.
11. Repeat the steps for all instances in your distributed environment before starting the Cognos Analytics Services and start the webserver
Cognos 11.2.4 End of Support: Why You Must Upgrade to Cognos 12 Before April 2026
https://www.ibm.com/docs/en/cognos-analytics/12.0.x?topic=analytics-upgrading-cognos
- Reviewing the documentation
Documentation is provided to help you achieve a successful upgrade. - Assess applications in your environment before you upgrade
Preparing to upgrade provides an opportunity to review your existing applications and clean up your source environment. - Install and configure a new version of the product
Install the new version of the product to a new location. The location can be on the same computer as your existing version of the product or on another computer. - Move your content to the new version of the product
There are two methods for moving your content. You can move the entire content store, or you can move content by creating deployment archives. - Upgrade your content store
IBM Cognos Analytics upgrades the content store database to the new version of the product when you start the services for the first time. - Moving your content with a deployment archive
To move specific content from your content store you can use deployment archives. Deployment archives are compressed files that you can then import into your new version of the product. - Upgrade your report specifications
Report specifications will have changed from one version of IBM Cognos Analytics to another. You must upgrade any report specifications created in previous versions of the product.