In general, I found Lightroom to be one of the most stable pieces of photo editing software. I've never encountered a problem with it, except when there was a computer or hard drive malfunction. This may or may not have been the case in your situation.
Whenever suddenly the ? and ! appear, generally it's user or computer error, not LR error. You say you are aware of the fact that you should not mess with your images in windows explorer, so that rules out that option. Unless you did something like it and forgot about it. From my point of view, it's likeliy that there was a hard drive failure or something else that caused your files to be moved from the one place to the other. I think the clues that you should be looking for are where the images have been moved to and why.
Reimporting can be useful in rare cases, but keep in mind that you will lose the edits you made to those images. Before reimporting an image, make sure that it doesn't exist anymore in your Lightroom Catalog.
As you have rescued your images already, there is no need for us to help you with that, but it would be useful to find out what went wrong and why. If you run a diagnostic test on your computer and something actually is wrong, it will not only affect your LR images but also other data you may have.
Finally, please have a look at
http://www.lightroomqueen.com/commu...765-Backing-up-Lightroom-All-you-need-to-know. With adequate backups, you won't need to manually fix the issue, but you can simply restore your catalog and/or your images from your backup. It will take you a little time to set it up, but may save lots of time in the long run.
Good luck!