When modifying a standard to remove a check in CCS, if you right-click on the check and select 'Delete', it sometimes deletes the entire standard instead of just the one row of the check.
CCS 12.6.X
When deleting a check in a CCS standard, do not right click on the yellow bar at the left end of the row (red arrow) to delete a single check (or row) as that is used to select multiple rows. If you do right-click on the yellow bar, when you select 'Delete' any row that is highlighted will be deleted, or even the standard itself.
If a single row is to be deleted, right-click on the white space before the check (green arrow) and select 'Delete', and that will clear any other rows that might have been inadvertently highlighted and will only delete that single row.
See the screenshot below: