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OBIA rpd upgrade from 7.9.6.3 to 7.9.6.4

Hi Team,
We are upgrading OBIA from 7.9.6.3 to 7.9.6.4. We are currently using Project Analytics from the OOB rpd and rest of them are customized in our project rpd.
Here are the steps I am taking to upgrade the rpd.
1. Extract Project Analytics from 7.9.6.3 OOB rpd (A). This also give Usage Tracking SA after the extract, so manually deleting it.
2. Extract Project Analytics from 7.9.6.4 OOB rpd (B). This also give Usage Tracking SA after the extract, so manually deleting it.
3. Custom Project rpd (C) has around 10 Business Model and 30 SAs, out of that only one i.e. Project Analytics Business Model uses OOB.
4. I open Custom Project rpd first using Admin tool 11.1.1.7.1, Select Merge rpd, Select A as original rpd, Select B as Modified rpd and C as Current rpd. And Equalize during merge
5. After the merge, in the pop up, I selected Current for the custom SA which is present in the current rpd and this gives me the upgraded final rpd (D).
Now when I compare between C and D, I should only get the upgraded change from Project Analytics.
But I also see some changes related to Variable, Init blocks for which it did not even ask me to select Current or Modified. There are few changes which are directly merged without asking develop to select.
Can anyone suggest if I am on the right track to upgrade the rpd.?
Regards,