If the colour of a channel is changed by selecting a different colour property and then the session is saved as a *.sr file, then when the file is opened the colour will have reverted back to the default colour so that the user choice is lost. This property data should be saved with the file.
I think we can consider this closed with https://sigrok.org/gitweb/?p=pulseview.git;a=commit;h=323715c41a09a1aba08f4b716e9d93da58f0f3a8 implemented. Thanks for your bug report, Paul Crawford!