What is the name of the file which contain database call in RPC SOAP client source code?
I don't think there is a file/class that makes direct call to database. In fact, the classes make use of available remote API methods, so you can only see the implementation of those.
See the example code for SOAP here - https://developer.atlassian.com/display/JIRADEV/Creating+a+JIRA+SOAP+Client
Then how it will update the database ?
Your SOAP client runs the remote method > This method sends request to JIRA > JIRA updates the database
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