Hi
I understand, I lived a similar situation and we ended restoring system (a lot of syntax errors in standard functionality in a 46B, before SNOTE), and the first task is retrieve versions or level versions (request ID in each object) in all systems. Please, see the document "SPDD & SPAU Adjustments Handbook" by Ravi Kumar Munagala in this site (link: http://scn.sap.com/docs/DOC-10312. As he says, the better option is store all adjustments (in SPDD and SPAU) in one request and transport it to destination systems. Of course,the requirement is that version in quality and production must be the same. Other issue is the object generated by templates (for instance, COPA reports and so on, as PA concern) in production, usually you run some reports and object are adjusted.
Read carefully the print files in help.sap.com or in this link: http://help.sap.com/printdocu/core/print46c/en/Data/htm/english.htm.
See basis components / upgrade general
and perhaps the most important (in my opinion), the print file with the title "changing the SAP standard (BC)" in the path basis components / ABAP Workbench (BC-DWB).
If you copy production to development, don't forget to save the versions management in development, be careful with this issue.
I hope this helps you
And the best of luck
Eduardo