Hello Philip
The upgrade tool will stop for the SPDD task. You can set the parameters in the shadow instance profile and restart the system before you continue from the SPDD phase. if you are using a transport request to perform the SPDD phase then you will can modify the shadow system profile from the OS level. The profiles will be created in the /<upgrade_directory>/abap/SID/SYS/profile directory. If the profiles are already created you can set the parameters in the profile and during the start of the shadow instance for the first time the system will use those parameters.
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Regards
RB