Decompiling and recompiling APK file

Question

I'm currently working on analyzing some android malwares and i need to decompile APK files. Reading an answer and many other answers like it, i know that we can extract java source code and other resources, create a new project and put those files in, make some modifications and compile the project. Is this approach applicable to every APK file ? If we aim to make very little or no modifications in the java source code, does this approach work for every APK file? If not, what is the main reason?

As another question, i remember i read somewhere (can not find it now) that said converting dex to jar (with tools such as dex2jar) or decompiling dex to java (with tools such as JADX) is somehow lossy and causes information loss. Is there any such concept?

I ask this questions for educational purposes and i'm not aiming to do anything illegal.