Use the advice given here to help
you to resolve problems when you delete resources.
You cannot delete a project from your workspace
Scenario: You cannot delete a project from your
workspace. You get error messages indicating that the containing directory
cannot be deleted, or the project file is missing.
Explanation: If you attempt to delete a project,
and the directory that contains the project is in use, or you have
any files that are contained within the project that have been opened
by programs other than the IBM® Integration Toolkit,
some of the resources in the project are not deleted, but others,
including the project file, might be deleted.
Solution: Before you delete a project, make sure
that other applications do not have the files open, and that you do
not have an open command prompt located in the directory. To recover
from this problem, manually delete any remaining files and directories
from your workspace directory, then click Delete from
the project in the IBM Integration Toolkit.