OK, if those paths are absolute paths, that is, they appear as C:\Test_Code\MyProject\Sources\... then the new project is going to use that absolute path information to go to the older folder. You want to have project relative paths, which appear as {CodeWarrior Project}\Sources in the access paths settings. A relative path lets the IDE select the active project directory and start from there in its search. You are seeing the IDE try to do the right thing when you search the currently open project.
No, what I meant by data folder is that you delete the MyProject_Data folder that appears in your new project's folder.
What I would try is this:
1) Go back to the original project. Make a copy of it. Name the copy something different, like New_Project.
2) Quite the IDE, then open the new project. Choose Project > Re-search for files and Project > Reset Project Entry Paths.
3) Quit the IDE. Go into the new project's folder and delete the New_Project_Data folder.
4) Restart the IDE and check the Access Paths settings. There should only be default paths, and they should be relative paths. If not, you have to delete the absolute paths.
---Tom