A warning is triggered when you launch an Intel-only app, and you will see it every time you launch such an app. Launching a recently used Intel app again won't trigger it, but if enough time has passed then you'll see the warning again for that app. For example, I last used the SynologyAssistant app to check on my NAS over a month ago, and launching it generated the banner message.

To avoid this issue you need to run only Universal or Apple Silicon apps. For apps that are Intel only, contact the developers and push them to release updated versions of their apps (but keep in mind that they have over a year before their apps stop working on macOS).
To see which of your apps are Intel and thus need to be updated or they won't run on macOS 28 (Fall 2027), hold the Option key and click the Apple menu, then select System Information (the top item). Select Applications in the Software section of the sidebar, then click on the Kind column header to sort them.

Some apps aren't readily identifiable by the name, but when you select that app you will get more info. For example, 'commandFilter' is a component of the Epson printer drivers. If you no longer use them, then apps like that can be safely deleted. The location to the application/extension can be seen in the report, to navigate to the app in Finder simply select and copy the above path up to and including the last / (but not the app name itself) then in Finder select Go menu > Go to Folder, paste the path and press return. As an example, the path to be pasted from the example above is:
/Library/Printers/EPSON/Fax/Filter/
Here's what Apple has to say about updating your apps:
Learn how to update Intel-based apps for Apple silicon - Apple Support