It's apparent master goes missing when noticing... (6)
I believe the answer is:
seeing
'noticing' is the definition.
(I've seen this before)
'it's apparent master goes missing' is the wordplay.
'it's apparent' becomes 'seeming' (synonyms).
'master' becomes 'M' (common abbreviation eg MA, Master of Art).
'goes missing' is a deletion indicator.
'seeming' with 'm' taken out is 'SEEING'.
'when' is the link.
(Other definitions for seeing that I've seen before include "... is believing, it's said" , "Noticing" , "Perceiving by eye" , "Watching" , "since" .)