With this new system variable you have better control on when and if layer filters should be deleted.
Saved in: Registry
Initial value: 2
Deletes excessive layer filters to improve performance. When a drawing has 100 or more layer filters, and the number of layer filters exceeds the number of layers, LAYERFILTERALERT provides a method for deleting layer filters to improve performance.
1 When the Layer Manager is opened, deletes all layer filters; no message is displayed
2 When the Layer Manager is opened, displays a message that states the problem, recommends deleting all filters, and offers a choice: “Do you want to delete all layer filters now?”
3 When the drawing is opened, displays a message that states the problem and offers to display a dialog box where you can choose which filters to delete
More about AutoCAD 2006 here.