IPhone – Will a restore to default factory settings remove the firmware updates from the Iphone

I believe all of the current jailbreak solutions work by modifying an IPSW file for the device, and flashing that back on to it. To remove it, you would need a clean IPSW and to do that you need to restore it through iTunes. If you don't back it up first (wether that be on iCloud or iTunes), then obviously you'll lose all of the settings, apps, and app data on the phone as well.

Firstly I would sign up to iCloud if you haven't and then use the over the air backup to backup your iPhone (You get 5GB free!) then once this is done, you will be able to reset the phone should you want / need to.

Have there been any updates to your Virtual Box since your last sync? If not, it could be that iTunes can not see its XML file needed for device synchronisation; also ensure that all of the helper services are started on your machine.

Failing the above and assuming you follow the first recommendation, try resetting and restoring from iCloud.

Best of luck