Making up is indicated, say after lunchtime (9)
I believe the answer is:
'making up' is the definition.
(atoning for something is making up for it)
'indicated say after lunchtime' is the wordplay.
'indicated' becomes 'meant' (I've seen this in another clue).
'say' indicates a 'sounds like' (homophone) clue.
'after' says to put letters next to each other.
'lunchtime' becomes 'at one' (at 1pm).
'meant' sounds like 'ment'.
'ment' put after 'atone' is 'ATONEMENT'.
'is' is the link.
(Other definitions for atonement that I've seen before include "needed to make amends" , "reparations?" , "Making good" , "satisfaction" , "Compensation for a wrong" .)