Well, you should be okay with the next boot, you can just swithc off the N9 and reboot to Nemo, and if all went okay you will get the graphical UI the next boot.

If you don't, then you would need to ssh to the device to find out from logs why it does not boot to UI.
(or it may be that it did not boot correctly at all, then you can look in your Harmattan side /var/log/ directory, you will find 2 files there; ubiboot.log and ubiboot.dmesg that should show you some info on the boot process...)

How to do that in windows; you need advice of somebody using windows, I am afraid I cannot help you there. The ubiboot wiki page http://wiki.maemo.org/Ubiboot shows some advice for windows users.