A client we have was having the files disappear when opening and saving directly to the server sharepoint. We would reproduce the error as follows:
1. Open .psd file from the server
2. Make changes
3. Save
4. If you receive the error message: "Could not save as "" because an unexpected end-of-file was encountered"
5. Click OK
6. File disappears from the server
7. Save again
8. Save As prompt appears
9. Same location is selected with same file name. The file saves correctly.
We resolved the issue by changing one setting, and it may also works for you:
1. Click Photoshop->Preferences->File Handling
2. Under File Saving Options->Image Previews
3. Change to "Never Save"
Give this a try, and hopefully it fixes the issue for you.
