If you can give specific examples, maybe people in the community can advise.
All of your listed scenarios, by their very nature, may augment, add, and even remove some previously expected behaviors.
Without specific examples, all that can be given is generally advice:
Plugins are meant to add/augment behavior. Sometimes a restart is required after doing either one as a plugin might not have everything loaded proper until after a restart. Check the console for errors, and report error to the plugin authors. Also read the plugin’s documentation to understand how it my augment your environment.
If you suspect a plugin is changing behavior of your editor in an unexpected way, try disabling the plugin and see if the issue goes away. If it does, you can always report the bug to the plugin’s issue tracker.
Read the changelog for new versions and see if there was a purposeful change you need to be aware of and how that may affect your workflow. Check console for errors. If they seem to be attributed to a plugin see (1), if not, you can create a thread here to get input from the community and/or file a bug report at https://github.com/SublimeTextIssues/Core/issues.
When editing a settings file, check out documentation on what the setting does, if it is unclear, ask in a thread here to get clarification. Check console as sometimes the settings file can accidentally become malformed when editing them and throw errors (though I believe a popup will usually be generated in that case).
As stated, this is just general advice, but please do post specifics, and I’m sure there are many helpful people who can answer your questions.