I am not sure about the proper ejecr process either, but I have always made sure that both the PC and phone are finished with I/O.
I tend to attempt to eject the device First from the tray icon and then stop USB mass storage on the phone. This works and I have never had a corruption.
If the PC says that it is not safe to Eject, I wait a minute and try again. If it still says this, I close phone USB and try it again. If the PC is still busy, I do an orderly shutdown of Windows. I wait how ever long that takes. After the PC is off, I unplug the phone.
Probably a little too cautious, but I don't want problems with the phone. I can't remember ever having this problem with the phone but it has happened with other Mass Storage USB devices. If it did happen with the phone, that is the procedure that I would recommend.
I must admit that many times in the past with thumb drives at work I haven't been that meticulous and just snatched the USB. But that was in cases that were not mission critical where a corrupted Spreadsheet would be obvious. So instead of shutting off the PC, I would just plug the thumb drive back in and try to load the file to check for corruption. Even then the copied file was almost always fine.