If you are trying to solve a specific problem that involves CRUDCRUD (create, read, update, delete) operations on some part(s) of some files in a structured file format, chances are good that the mechanism you're going to use to solve that problem is some kind of code (programming).
If the code you're writing is in a common scripting language typically used by power users and system administrators (say, cmd.exe, bashBash, powershelland PowerShell), it's leaning to be on-topic for SuperUserSuper User.
If the code you're writing is in some kind of "serious programmers" context (C#C#, C++C++, JavaJava, anything server-side, etc.), it's leaning to be on-topic for StackOverflowStack Overflow.
If you're not writing code at all, but rather, using some kind of pre-built tool to manipulate the data, it's very much on-topic for SuperUserSuper User.
For instance: if you are using RegexBuddyRegexBuddy to work on a regular expression, and you have a question either about RegexBuddy or about your regular expression (but not about the code that you'll write to use the regular expression), it's topical for SuperUserSuper User. If you want to know how to use the regular expressionregular expression API in, say, Java, that's topical for StackOverflowStack Overflow.
In between these extremes there are many overlaps and gray areas. In general, you will probably get better answers about the nitty-gritty of binary file formats from StackOverflowStack Overflow users (to say nothing of the fact that on SOStack Overflow you have more people looking at your question than on the comparatively small SuperUserSuper User). But, just because you get better answers there, doesn't mean it's off-topic for SuperUserSuper User.
In fact, it might be on-topic for SuperUserSuper User, but our user base might not have a great many people who are familiar enough with the subject to be able to answer efficiently without a lot of learning / googling on our part.
But remember, it's fairly likely to get closed or migrated if your question is just a pastie of "real programmers' code" asking people to fix your problem. Conceptual questions are much more likely to be accepted here. Human-readable file formats, like XML, are also extremely on-topic for SUSuper User, since many system administrators tend to deal with XML configuration files of various sorts, and they can be edited using a simple text editor.
To close, I should obviously mention that we are not to discuss what is considered to be topical on SOStack Overflow, on Meta Super User. SOStack Overflow has their topicality boundaries; SUSuper User has our topicality boundaries; and the two are free to intersect (or not) however the respective communities please. Anything in my answer here that implies certain facts about SO'sStack Overflow's topicality should be taken with a grain of salt, since I am not a significant participant on SOStack Overflow. I can only accurately speak to the topicality of SUSuper User. If you have a question specifically about what is topical on SOStack Overflow, ask it on Meta Stack Overflow. All we can do here is affirm what SU'sSuper User's topicality boundaries are.