Getting your rooted 2.2.1 Commando to update is simple, really. First make yourself a sandwich and grab a cold beer, you're going to be on the phone for a while. Call 1 800 922 0204 from another phone. Once you make it through the layers of automation and actually get to a human, explain that your Commando won't take the update. They will have you do several things, including a hard reset. Eventually they will wear down and offer to send you a replacement, Certified Like-New device. Accept their offer and then decide what kind of shipping you want. They will charge you for over night and two-day shipping via FedEx, or you can opt for USPS First Class mail. Depending on how far you are from Ft. Worth, TX, USPS will be fine. It took two days for the replacement to come to Florida. While you are waiting go ahead and restore all of the carrier apps, delete the busybox from the xbin folder and then unroot the phone.
When your CLN device arrives, activate it and then follow paxchristos' guide to rooting the 2.3.3 commando. Very easy, works as described.
Oh yeah, be sure to send your old phone back or they will make you buy it at full price.