I did 350 from 9.0.3.34 to 10.0.4.26/MCD 4.0 SP 4 with 5 that failed. 3 of those were due to the site losing power between the start of the upgrade and the activation time, and 2 failed "safe" in that they didn't activate the new release and stayed running at 9.0; a 2nd attempt on those worked.
You will still use the SI tool to initiate the upgrade, except you will point the MCD towards the MBG (FTP server) instead of an FTP server located off site. Keep in mind that the online upgrade will format your inactive partition and restore the backup file which is generated when you start the SI process. Any changes made after the restore which are made to the active partition will not carry over.
How critical is it that the site remain up for the entire process? I find that the biggest delay in upgrading is actually getting the files to the controller. If you've got them onsite on the MBG, an offline upgrade should go relatively quickly.
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