First officer left it out initially with folded sheet (5)
I believe the answer is:
folio
'folded sheet' is the definition.
(I've seen this in another clue)
'first officer left it out initially' is the wordplay.
'initially' suggests taking the first letters.
The first letters of 'first officer left it out' is 'FOLIO'.
'with' acts as a link.
(Other definitions for folio that I've seen before include "Two-leaf sheet" , "Book size" , "Sheet of paper folded to make two book leaves" , "Body of written work" , "outsize book" .)