Performing SPAU in Production System

Dear Team,
We are in the process of upgrading our Production system from EHP3 to EHP7.
We upgraded our Quality system with SPDD and SPAU transport requests from Development system and it finished successfully.
But after upgrading our Kernel in Production system and before performing the EHP7 upgrade, we applied two SAP notes in Production system, these notes were transported from our temporary development(un-upgraded) system(parallel landscape).
While performing the EHP upgrade in Production system,  SUM has prompted us the below message
“Decide about Incomplete Modification Transport”
CAUTION: The program has found the transport "MEDK906662"(our SPAU transport) for SPAU but it does not contain all objects which need adjustment.
When we checked the log file it show that two objects are missing in the SPAU transport.We suspect these are the SAP Notes which we applied after kernel upgrade and are missing in SPAU transport request.
Please let me know how we can correct this issue in Production system. I know that SPAU will appear in Production system, but will the system allow me to re-apply/reset the SAP note in SPAU as this system will be un-modifiable.
Regards
Imran

SE06.
System Change. Global setting "modifiable". Componenents "modifiable". Namespaces "modifiable".
Client setting-> select client -> Automatic recording of changes, changes to repository and cross-client customising allowed, protection level 0.
If that doesn't work, give yourself SAPALL and try again.
If that doesn't work, contact SAP because something is messed up. I've successfully applied notes in P systems during upgrade. Including ones that modify SAP_APPL.

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