Depends on where you are doing the "edit". Assuming you're working in a plugin of some sort, the process you are doing the edit in is likely to give you an issue object (in fact, a mutableissue object), and you'll need to update the fields in that.
Some gotchas though
There's probably a lot more people could volunteer for you, but you really need to give us a lot more information on what you'd like to have your work do, and where it's running, and so-on.
I need to look-up a series of issues by key, and edit 2 custom text fields. the fields are otherwise read-only to the user, and cannot be modified in any other way.
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