I recently had a computer meltdown and had to re-install VSD on another computer. I made some changes to one of my sites today and had to upload for the first time since the new install.

As I'd forgotten my FTP settings, I accidently uploaded my site to the root directory, instead of the correct sub-domain, and overwrote my other site. I deleted the incorrectly uploaded files manually, then re-uploaded the root site again, which fixed that issue. Then I altered the FTP settings and uploaded the sub-domain site again - that's where it got weird.

For some reason the pages that I had edited/added today uploaded correctly into the sub-domain directory, but the remainder of the site was again uploaded to the root directory, and all other pages in the sub-directory were deleted. I can't figure out what I did wrong - I can't even see how I would have been able to replicate this action.

Long story short, I re-deleted the offending files from the root, then did a re-sync on the sub-directory (without altering the FTP settings from the last attempt) and it has worked. I'm only mentioning it just in case someone else has a similar issue and wants to know how to fix it.

Now I just have to re-sync the root site successfully and all will be well in my world again .

That's great Cogsy,
I just replaced my hard drive recently and had to reconnoiter my site also. I didn't have any of those issues because I selected re-sync at first upload. Thanks for sharing your experience.