Upgrade from 9900 to 10250 question

Should rawcleanup.bat take some time?

Also I'm following the instructions to upgrade but it's not clear. There are two files to download. One PPM for 10250 and another for the JVM upgrade to 7. However it then mentions the following. At what point do you update the JVM? The following just appears to imply you just point to the PPM for 10250.

Execute the UpdateManager.bat (.sh in case of Linux) file present in the /bin directory.
From the window that pops up, click Browse and select the service pack you downloaded.
Click Install to install the service pack. This may take several minutes depending on the amount of data that needs to be migrated.
Wait until the service pack is fully installed.
Click Close and then click Exit to exit the Update Manager tool.
Start the NetFlow Analyzer service.