As topic above i have multiple WordPress site and each site got different site color.
After i clone Master to sub-sites and i change theme color on Ajax Search Pro on sub-sites, seems all site included Master will changes into that sub-sites which is not intended.
The same search bars are available across the multisite, they are global. If you change a setting on a search instance it will affect that same search bar across all of the network – which is intended behavior. Otherwise search bars would not be possible to use across the network.
I recommend rather creating multiple search bars if you want different configurations, or using custom CSS to change the colors on specific sites only.