Color is tied to the values that exist within the view. When values are filtered out then the color tied to those values can change.
If you are using a quantitative measure on color, then you can lock the color into a certain range, which should preserve the right colors for positive vs. negative. Here are some quick instructions and a link to the product guide on color:
1. Click on Color > Edit Color on the Marks card.
2. Click Advanced >>
3. Set Start to the minimum value that is expected or could occur
4. Set End to the maximum value that is expected or could occur
5. Click OK