There are some things you definitely can't do to these system fields - you can't rename system fields, for example.
If you're trying to update the values/options for these system fields, that depends on the field.
If this doesn't answer your question, what kind of changes are you wanting to make to system fields?
Labels in Jira are pretty much free-form. Any user in your Jira instance can create a label or use an existing label. There's very little governance around labels, and I don't really recommend using labels for anything other than short-term categorization/reporting. Labels shouldn't be used for anything permanent, in my opinion.
The Jira database should never be modified directly. Doing so can have significant negative ramifications on the health of your Jira instance.
For the Labels field, if at least one issue in your entire Jira instance is using a label option, that label option will be available in your entire Jira instance. The only way to remove a label value is to remove that label option from all issues in your instance. Even so, there's nothing stopping any user from just recreating the label option since the Label field is completely free form and available for anyone to add any value they want.
Why are you wanting to remove label value options? It sounds like you're trying to implement something permanent, and I don't really recommend using the Label field for any type of permanent categorization. I'd opt for custom field with pre-determined values instead.
If you're looking to replace the existing option with your required option, you can use a bulk edit to find and replace label values.
Bulk edits are generally capped at 1000 issues at a time by default, as well. You can increase this amount, but I wouldn't increase the cap by much (if at all).
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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