OK, I've probably done something close to what you have done.
You can do exactly that, import the ICO file into another project. If you're using an ST board (disco, etc), you may want to set the pin assignments to default, since that tracks the actual board hardware (which is not always the default settings, which can change)
Since you can't have a project with two main.c files (or shouldn't!), it sounds as if when importing the IOC file, you created a new project in the same directory as possibly the old one, or at least, the same workspace.
You might want to check where things are, and remove the older project. Eclipse will allow multiple projects in a workspace, but I tend to avoid it.
A preferred (because it works) structure is to have a directory which has a folder of "subsystems", which contains all the files I use, system files, driver files, specific hardware (I do use an RTOS), categorized as I like.
I have a separate folder at the same level as the subsystems file, called "projects" which contains each particular project workspace. That also contains the main.c and all the other files needed for that project.
To make a new project, I set up a blank folder within projects, then set the workspace to that. I then either generate the IOC file or do a new project based on the IOC file, making sure that the project location created is the newly named file. I add stuff as needed (I do a lot of #ifdef) in an "options.h" file which is in the "core" folder, but not the inc or src (you need to add paths as needed).
Then I can take the entire subsystems folder and drag it from the file manager and drop it on the top level project. Tell the system to create links, rather than copy. Go to the subsystems folder and look at the properties. Make sure the "exclude from build" is NOT checked (don't ask how I found this out). The other files under subsystems should follow this.
Rebuild index as needed. Delete unwanted file links from under subsystems as needed, note that it's all links.
You'll always be working with your original files, not copies, so you need to be careful when making changes to your "standard" files, etc.
Perhaps this will help.
