Rainbow color settings does not recovering after JIRA appication restart, but application properties is in place.
JIRA 7.3.5, Service Desk 3.4.2
I can't reproduce this. I have stoped and restarted the system again and again and colors persist. Actually these values are stored by Atlassian's own API as you can see they are stored in general table where rest of other add-on and Atlassian's own data persisted. It may be related with killing the server. Why don't you just use ./stop-jira.sh script? Meantime I can release ability to enter color codes manually and this may help you to restore lost color values.
It's getting annoying that we are loosing the color settings and clients is kicking the ass after every drop of the color configuration. Please, investigate more on this issue. Maybe it's not related to server kills, but on the data inconsistency in the application or some duplications. I think that there is the catch why it's returning the default settings.
Could you test to stop jira using the ./stop-jira.sh script instead of killing it? Since I can't reproduce the problem I can't fix it. May be I can write a script to export and import the colors, so that they don't have to manually specify the colors.