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The only way is to purchase Titanium Backup and use Market Doctor but you have to be rooted.

You don't need to root in order to do this.
Just use AppBrain!
Yes, you technically have to reinstall all the app's again, but at least they are all in one place. Just load it up, hit sync and then "install all". And since they are technically now new installs, you will continue to get updates on them.
Working on it now. Didnt even know appbrain had that option.
Appbrain is showing that 3 apps have updates; Adobe flash, Amazon MP3 and scanner radio but when I got to the market to update it doesnt show they need to be updated (flash doesnt even show as downloaded). Any ideas?
make sure you make a new list on app brain wth all the apps and then choose install list bc app brain will delete them if its not in a list once it syncs
Like I said, the only way is to root and use Titanium Backup and Market Doctor.
App brain does not fix the Market sync/update issue.

It didn't work for you?
It's what I did on my phone and my fiance's and it's working just fine. We still get updates like we always did. It's different than using Astro since it's only a database of your apps, you are still doing a "fresh install" of them after you reset.
It's no different than using pen and paper to write down all of your app's and then reinstalling them from the market.
Edit:
Ok so it worked for reinstalling applications fresh, but not if you want to transfer an .apk in which you want it to recognize that you downloaded it in say, June or July to retain free 'grandfathered' rights..
In that case I use Titanium while rooted and then use Market Doctor so that I can receive updates on a grandfathered app (shazam, nfl mobile, etc..).
Good to know. I'll use this for apps that I want to reinstall fresh.

It's pretty simple actually.
BEFORE reset:
Download App Brain app and hit sync all. All your apps will go to a list called "apps on the phone".
AFTER reset:
On your PC - Go to appbrain.com and log into your account. You will now see another folder called HTC Droid Incredible. Open your previous Apps On The Phone folder, hit select all, then move them all to the new folder.
Go to the market and download AppBrain app. Open app, hit sync all and then preform installs.
Once all of your apps are reloaded, go back and delete the "apps on the phone" list, you don't need it anymore.
It's pretty simple actually.
BEFORE reset:
Download App Brain app and hit sync all. All your apps will go to a list called "apps on the phone".
AFTER reset:
On your PC - Go to appbrain.com and log into your account. You will now see another folder called HTC Droid Incredible. Open your previous Apps On The Phone folder, hit select all, then move them all to the new folder.
Go to the market and download AppBrain app. Open app, hit sync all and then preform installs.
Once all of your apps are reloaded, go back and delete the "apps on the phone" list, you don't need it anymore.