fs_clone is not related with autoconfig. fs_clone copies the run file system to the patch file system.
There are several cases where you may use it.
Read this :
http://ermanarslan.blogspot.com.tr/2016/05/ebs-122-sync-errors-due-to-missing.htmlexecuting fs_clone is actually useful some other cases as well. As documented in E-Business Suite - ADOP Basic Usage Training Videos [Video] ( Doc ID 2103131.1 ).
Sometimes we can even execute fs_clone by our own decision to decrease the job of the next prepare phase