In SQL Server Data Tools (SSDT), you can delete packages listed as saved to the file system. If you delete a package, it is deleted permanently and it cannot be restored to an Integration Services project.
If you want to remove packages from an Integration Services project, but use them in other projects, then you should use the Exclude From Project option instead of the Delete option.
To delete a package in SQL Server Data Tools
In SQL Server Data Tools (SSDT), open the Integration Services project that contains the package you want to delete.
In Solution Explorer, right-click the package, and then click Delete.
Click OK to confirm the deletion or click Cancel to keep the package.