As long as your device still boots you should be fine.

You mentioned that you have already flashed the N900 before, but did you really flash the full PR 1.2 firmware and the PR 1.2 vanilla eMMC image to the device?

Have a look at this wiki section for more details. I strongly recommend to use Linux (try Ubuntu) for flashing images to the N900, as I've had problems on both Windows and Mac OS X.

Please make sure you flash the actual firmware image (without -R) and the vanilla eMMC image right afterwards, just like it says in the wiki.

If this does not help then the device's flash memory might be broken somehow, which would be bad.