Hi Imran,
Please never add or remove Logical Components for active project cycle, this is always dangerous.
If you would like to add/remove Logical Component to project landscape or to manually adjust systems (change systems and roles) included in exiting Logical Component for active project cycle after the task list generation, I would recommend always follow the following steps:
Close the current project cycle
Add/remove Logical Component
Generate a new project cycle
Any change in the TMS configuration, in the transport routes for example, will be handling in the same way.
Thanks
Vikram