I will answer based on the understanding that the color change is not reflected when categories A and B exist in the properties and the following actions are taken.
Step 1) Select category A for the axis of the graph, and change the color using the color criteria.
Step 2) Select Category B for the axis of the graph and switch categories.
Step 3) When category A is selected for the axis of the graph, the change in step 1) is not reflected.
Thank you for sharing this idea. If I understand correctly, you're referring to the color scheme applied to a Color-by axis, and you expect Spotfire to retain the custom color scheme when switching the Color-by axis back and forth between different columns. Is that right?
There is a way to set a custom color scheme for a particular column, which might help with this scenario. You can check out the step in this knowledge article.
Looking forward to your response.