Can you give a little more detail about what happened? The way I'm reading your original post, you used Windows File Explorer to copy an assembly file from one project folder to a different project folder. But I'm not clear on how you "made modifications to this file". I'm afraid that you made modifications to the components of your assembly, which you didn't copy along with the assembly.
So, here's how it should work. You should have a project file (.ipj) that defines the workspace where that project's files are located. When you want to copy to a new project, you make a new folder and create a new .ipj file in that one, then copy your assembly and all its components to that folder, then change your active project to that new project file. Now when you open your copied assembly, it can't "see" its original component files in the old project folder, it can only see the copied ones in the new folder, because the project file determines what folders are available to it.
Post back if I'm misunderstanding, or if I what I wrote isn't clear. Unfortunately, learning things the hard way is often the most effective way to learn!
Sam B
Inventor Professional 2017 R2
Vault Basic 2017.0.1
Windows 7 Enterprise 64-bit, SP1
Inventor Certified Professional