You should do a factory reset, or you'll get intermitant crashes most likely.
Thats the anoying part about updating, you have to reinstall everything, and market is really crap at remembering your apps - sometimes it does, sometimes it doesnt.
Just remember the first time you open market (after wipe) go to my downloads and re-install everything there you want. If you close market it'll forget everything! So don't go to the home screen at any point untill everything you wanted is installed.
I suppose the alternative would be to use that backup app for root that lets you backup your installed APKs.