Legacy projects tend to accumulate files that are no longer needed in the projects. These files are still on your disk, or even in your revision control system, but the scripts don't feed them to the simulator or to the synthesis tools any more. These junk files can accumulate over time as:

• stale copies of files that are still in use
• auxiliary files that are only intended to hold code snippets for cut-and-paste reuse
• old or broken files that did have a function once, but don't any more.

Junk files can accumulate in legacy projects
The recommended approach is to remove these junk files. If you are using a revision control system, you can always go back, so there is no risk to removing stale files.

However, if there is a good reason to keep junk files in the project folder, you can unmap them from all libraries: Right-click the files and select Library Mapping > Unmap.