To assign the missing status to a physical item, you must have the Physical Inventory Operator or Physical Inventory Operator Extended role.
Perform a Physical Title or Item search, then click on the ellipsis to the right of the item entry (Ex Libris calls this the "row actions list" and select Items.
Toggle Missing Status will be available from the row actions list at the end of that item’s row, unless the item is on loan or another process that would make it unavailable for circulation.
To mark an item missing that is loaned or in-process, first remove it from a user's account, or a work order, or an Alma process (Lost, Technical - Migration, Transit, etc.).