Hi,

PEP maintains one copy of your command set within your project (that's where you assign the button commands from) and one in your device database.
If you change/re-learn codes in your database, the project codes are not automatically updated.

This is probably what causes the yellow exclamation mark icon.
When you hover the mouse cursor over the icon, a popup will appear and - I suspect - tell you that the codes in your database differ from the project codes.

To solve this, click on the yellow exclamation mark and a window will appear, showing the differences between the project and the database codes.
In the center are two "arrow" buttons, "update project from database" and "update database from project".
Click the "update project from database" button to synchronize your newly learned codes to your project file.
This should immediately change the exclamation mark icon into a green checkmark.
There's also an "apply to all" option to speed up the process - be careful with the sync direction when using this.

Sebastian