That is what Alway Sync essentially does. Simply copies the files from one drive to another.
BUT - I don't even need to copy the files. I can go home right now, not copy anything and just open the web site in VSD and click "publish" Technically it should upload everything for "That" web page. - Instead it removes needed pic files and the index.html file. the second time I hit publish it puts the index.html file back on, but not the images. After that I can make changes all day long and publish just fine, from that computer. Once I come to work and open the site in VSD and hit publish, the process starts all over again.

I really don't think it matters how the files are being copied, but instead how VSD keeps track of what items was updated. another issue I noticed but wasn't a big deal, there are always 3 or 4 files that will upload every time I click publish even if nothing changed. Usually these are image files but sometimes they will be page files or other things. My www.royalephoenix.com web site will upload the same button image file every time I publish, for every page, for every button. If I go to my site using FTP there will be thousands of copies of my button images because it creates a new image and uploads it every time I click publish. I'm thinking this issue is related to how CC handles updated material, not very well.

Still can't figure this out. Vary agitating. Going to open a support ticket

I've had the same issue. If I publish from one computer, get everything right, then try to publish from another computer the entire site will come out scrambled. Pictures and icons seem to take on a different image tag and I can have pictures turn into icons or icons that stretch out many times their size. I've tried the resync the site button with the same results.
Usually I end up deleting the .vnu file from the server then re-publish and all comes out fine. Just a hassle.
Now I always do any updates from the same computer.

Yep. Support ticket was no help, just told "that's how it is". I'm finding a lot in CoffeCup software that does not operate as expected in all of there programs. Out of the hundreds of programs I have used over the years I have never had this type of issue, even with other web site software. Frankly, there is no reason for this NOT to work as one would expect. I'm finding I am using other software more and and CC less. Some of it still comes in handy like Web Image Studio - but even that is a pain to use because arrow keys and delete key do not operate as expected.

I am wondering if this may have something to do with the files not being in the exact same file structure on both computers? Many times different computers and operating systems have different default profile names for the computer directories and that can cause issues with swapping files between computers for various projects in various programs. Same thing if you don't keep the exact same file structure for your documents folders too. Not sure that's the problem, just offering a possibility to check out.

That is exactly the problem - However any other program out there looks for supporting files within it's own directory What point is it to copy image files to a "files" folder within it's own directory if it does not look for those files in that location?
So after opening "my_Website.vnu" it should look for support files starting from that directory, it should not care what computer it is on. This is how any other software works.

Actually, now that I think about it, that really isn't the issue. I'm not making the change, saving to the other computer then trying to upload them. I make the changes from the same computer I'm uploading from, the only issue is it was last updated from the other computer. In fact, I don't have to make any changes. Just upload and it erases my image files form the server - why, because it was uploaded from a different computer? that makes no sense at all.

The only way it will work if each computer is setup the exact same way with the way you are doing it. Same user and file locations. If you built a website and placed all the files you used on a flash drive before you added them and browsed to them on that when you did add them it should work. Also do a save as to the same flash drive.

That still don't explain why on the first publish it deletes the index.html file and all images from the files folder.

Lets start from the beginning and pretend nothing is loaded to the server.
Computer 1: I create the web site and save it then publish it to the web. No files are uploaded yet so it uploads all the files needed (all the ones within it's own directory, after all that's why it copies images to the files folder is it not?). Subsequent publishing form this computer uploads only changes. Well, kind-of. For some reason it will make duplicates of the same image and upload it several times. I'll end up with 50 or 60 copies of the same image - but that's a different issue.

Now I copy that to a USB drive and take it to computer 2 and copy the .vnu file and the website folder it to computer 2.

Computer 2: I open the file, all files are there, and at this point as far as the program is concerned I could have built the web page on this computer. I click save and then Publish. Now why is this any different that if I created an entirely different web site and published it to the same location - would it not upload all the files? But this does not, it instead deletes files. Also, why does the program care where the files that are already on the server came from? Lets say the site needs "pic1.jpg" - the file is already on the server from computer 1 publish, so why does the program delete the file? Publish should just publish the site, if the files aren't already on the server, then it should copy them there, but instead it deletes the files, it even deletes the index.html. A second publish will up load the index.html file but still not the pictures. A third publish does nothing. It should see that the needed pic files are not there and upload them. It should be uploading them from the folder that matches the .vnu file. Are you telling me that the program is uploading them from their original location and because it doesn't find them it don;t get uploaded? If that is the case then what is the point of coping the image to the files folder - useless.

I just don't get it. CC should work just like any other program.

Don't copy do a "Save as" to the external source.