Official replacing top of substantial shelter (6)
I believe the answer is:
refuge
'shelter' is the definition.
(I know that shelter can be written as refuge)
'official replacing top of substantial' is the wordplay.
I cannot quite understand how this works, but
'official' could be 'ref' (match official in football, say) and 'ref' is located in the answer.
This may be the basis of the clue (or it may be nonsense).
(Other definitions for refuge that I've seen before include "Place of safety" , "'Sanctuary, asylum (6)'" , "Traffic island" , "The sort of shelter" , "Shelter or protection from danger or trouble" .)