A little bit like this question How to lock compiled Java classes to prevent decompilation? , However I am well aware of how to decompile an application and try to understand it even if it is obfuscated but one thing im not too sure about is how the same process would work if the application loaded C libraries (.so files) using jni.
For example say if there was a calculator, if this calculator was built in pure java it would be possible to go in and mess up the square root button so that when you passed in 2 it would give back 2^3 rather then 2^2.
Now if this application used JNI to do all this math commands (so it passed the 2 to a native method), how would you be able to go into the C, change it so that it returns 2^3 and not 2^2?
Decompilation is older than bytecode. Pretty much everything can be decompiled. It’s definitely harder (both to decompile and to understand/modify the result) with mangled, optimized machine code with zero metadata preserved, but nonetheless possible. Of course you’d need a different decompiler, and – as hinted before – it would be a bit harder, but the fact (which makes all DRM tools imperfect, by the way) “if their CPU runs it, they can modify it”, holds for native code as much as for any bytecode.