Accounting periods: company accounting periods: superseded AP - unrelated assessment
When you use function MAPD (Maintain AP Dates), COTAX tries to link a superseded AP to a new superseding AP ending in the same link period (Word 28KB).
If it cannot, it asks you to provide the link. See COM1090 for more guidance.
Where, exceptionally, you conclude that there is no AP ending in the same link period as the period covered by the return, COTAX shows any CTSA assessment stranded on the superseded AP as an outstanding item.
As you have already considered assessments on superseded APs during the manual linking process, you should be able to use function RAMA (Record / Amend Assessment) to discharge any unlinked charges remaining.
See COM1021 for a list of functions to use in particular situations.