I have a installer app with a embedded .resx file with some information, like server name, port, password etc... I have to generate this installer (this process is automated
You are missing out on a fairly obscure detail in a C# program. The executable the compiler generates also contains unmanaged resources. Required because Windows doesn't know anything about managed resources. This is something you can see with Visual Studio. Use File + Open + File and select a .exe generated by the C# compiler. RTM edition required, it doesn't work for Express.
You'll see at least 3 nodes for your program:
RT_MANIFEST contains the manifest for the executable. Very important on later Windows versions, it declares the program compatible with UAC. It prevents Windows from treating your program like an earlier Windows program that needs to be lied to when it does UAC verboten things like trying to write files to protected directories and trying to create registry keys in HKLM. The content of the manifest is a default one in most programs, you can get a custom one with the "Application Manifest File" project item template.
"Version" contains the version resource for the executable. It contains the info you see when you look at the properties of the executable with Windows Explorer. Its content is auto-generated from the [assembly:] attributes in your AssemblyInfo.cs source code file.
"Icon" contains the icon resource for your program. The one you don't have anymore.
You'll need to use the /resource option for ilasm.exe to embed those unmanaged resources into the patched executable. That requires a .res file, the compiled version of the unmanaged resources, produced by the rc.exe Windows SDK tool. Note how this is also exposed in the Project + Properties, Application tab, Resource file radio button.
You cannot ignore this requirement, you can live without the Icon resource but not the manifest, especially not in an installer program. Getting the .res file out of the original executable is going to be difficult, fairly sure that ildasm.exe doesn't support decompiling it. If a tool like Resource Hacker doesn't do it then you'll need to create a .res file for your program. Or review the wisdom of using ildasm.exe to do what you wanted to do.