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If you follow the steps of cloning from (Cloning Oracle Applications Release 12 with Rapid Clone (Doc ID 406982.1)) then the $CONTEXT_FILE and $CONTEXT_NAME should have the correct values which is taken care of by Rapid Clone and you don't have to edit the target apps context/env files manually.
You need to review the value of "s_applptmp" in the application context file -- See (Difference between APPLPTMP and APPLTMP Directories in EBS (Doc ID 1355735.1)) for details.
Also, you shouldn't update the env file manually. If needed update the context file and run AutoConfig and this should be sufficient.
ok Hussein. This is almost certainly the correct answer I just need to verify my results before I give you full credit.
Well I still don't why this seems to be hit and miss for me (some environments work some keep prod's value) your solution is valid so I will close this post.