Installing Programs in Extended ROM

[answerman]

OK, finally bit the bullet and unlocked/cleared out my Alltel Extended ROM with my last flash to 1.0.2. Love having the extra 9.9MB of storage... I installed a few big programs in there and it all went great.

Now, the question. If I was to reflash 1.0.2 or whatever new version may come out, or just hard reset for that matter, what happens to the programs I installed in Extended ROM? I assume that the files will still be there after a reflash, but I would have to reinstall them from the cabs since none of the registry keys will exist anymore.

Assuming I am right about this, what's the best way to go about it? Do I need to clear out the files first, or can I just reinstall them over the existing files?