Make certain changes to username, though not in the morning (6)
I believe the answer is:
ensure
'make certain' is the definition.
(synonyms)
'changes to username though not in the morning' is the wordplay.
'changes to' indicates an anagram (I've seen 'change to' mean this).
'though not' is a deletion indicator.
'in the morning' becomes 'am' (short for ante meridiem - before noon).
'username' with 'am' taken out is 'userne'.
'userne' with letters rearranged gives 'ENSURE'.
(Other definitions for ensure that I've seen before include "Make certain that (something occurs)" , "warrant" , "Make certain, clinch" , "Make certain (something will occur)" , "Make certain, confirm" .)