I wonder if you have a bug in your diagnostics updating code. If each role ran code in OnStart or Run to configure diagnostics on startup, there would be no reason that your instances wouldn't be properly configured. I tend to think that imperative code that configures diagnostics is inherently a bad idea in the long run, but it should still work. If you share the code, maybe I can spot an issue.
The best** way I have found to update and enforce configuration is to use the diagnostics.wadcfg file and update it. When you upgrade your deployment, it will use those settings if you have not overridden it in code somewhere. Contrary to Microsoft's guidance at that link, it should be the preferred method as opposed to code which must be maintained and is orthogonal to your application's purpose. Said another way - a declarative configuration file that your ops team can maintain over writing code is usually a better idea. To use this, just include it in your deployment as content and delete any existing files in wad-control-container (and remove any code that configured diagnostics). It will just configure itself from that file then when you next upgrade.
** you can also using a 3rd party SaaS monitoring to set and maintain your diagnostics config. I work on one such one, but I am guessing you want to know how to do it yourself. :)