Obfuscation transformation and code maintainability
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.