Obfuscation transformation and code maintainability This is more a software engineering question, but my interest is in the mathematical modeling of the problem. 

While there seems to be some literature on the modeling of obfuscation transformation, I'm finding it difficult to locate papers that relates it to code maintenance - guess because they are inherently orthogonal. But its hard to imagine no study has been done by modeling this as an optimization problem. Can anybody point me to any thing that is helpful to get some insight into this?
From comments ...

Do you mean relation between code obfuscation and code maintenance?

Obviously good obfuscation means poor maintainability, so an alternate question is: how can a small part of the source code be reobfuscated without having to obfuscate the whole source code again? This leads to: "how can I build an efficient incremental obfuscator?" ... unfortunately obfuscators heavily depend on the target programming languages, so I don't think there are many academic papers on that subject.

However, if you need a more theoretical approach then you can start with a survey on the subject: for example: Code Obfuscation Literature Survey (with good references at the end). Or look for papers which cite the negative result of Barak et al.: On the (Im)possibility of Obfuscating Programs . 

Otherwise - if you are more "code-oriented" - you can search for information (and source code) on how real incremental obfuscators work (.NET obfuscator, ProGuard obfuscator, ...). Some years ago I used ProGuard to obfuscate a Java application (in Netbeans environment); it is an open source project, so you can download the full source code (http://proguard.sourceforge.net/). Incremental obfuscation is obtained keeping a mapping file that allows to mantain classes/variables/methods/etc.etc. names consistent across subsequent builds.