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Are you using the most recent version of Tableau Desktop (and Server) 10.3? There are a few bugs related to custom color palettes breaking and many of them were fixed in recent releases.
If you are on 10.3.9 already, or if you upgrade and it still reoccurs, I would recommend contacting Technical Support: Support Case | Tableau Software
I was able to get the color schemes to remain after republishing. I'm not sure what the issue was before, but it's resolved now
Whatever happened I'm glad that's fixed for you!