If you see a greyed-out checkbox next to a library, such as ecoinvent 3.6 Cut-off below, then you are not able to remove it directly. You need to consider the possibilities underneath.
To be able to remove a library from the library list in your SimaPro Flow project, you need to make sure that:
You are not using that library in your own project. You can check if you use any processes from specific libraries by going to Processes, click on the Library processes used tab and filter by the library you want to remove.
You are not using a company library which is using that library. In that case, you need to update the company library or create a copy of the company library which is updated.
Do you want to know more about how you can use the library switch? Check this article.