I'm currently not sure if it's OS depended or file system depended, but on Linux with one of the recommended file systems file names are case sensitive. That means that 'File1' and 'file1' are different files!
I am with you: the overwrite problem seems to be from WinXP. It can not differ between .jpg and .JPG. Users of FileZilla should be warned for this problem, when creating backups. Maybe it exists, but I did't read it

To recover the overwritten/missing pictures I'd do the following (regardless of your description). Just have a look which files are missing. Then upload that files with the same file names (including the same case). Now you should be able to see the full-sized version of that pictures. If that works, run the admin tools to create the intermediate-sized pictures (if needed) and the thumbnails. Don't try to rename that files with edit_one_pic.php.
Yes, it works: renamed original file 14.JPG from CD to 14~0.JPG and uploaded it beside 14~0.jpg. Now the Fullsizepicture of 14~0.JPG was visible, but not the thumb. Therefore I ran the Admintool "Update thumbs" of that Album > Thumb available.

Thx, André
I have to do this for the around 70pics. The Admintool "update thumbs" gave me an errorreport like this.
Extract of run1: "...
ERROR creating: albums/userpics/10001/thumb_16~0.JPG
albums/userpics/10001/thumb_15~0.jpg updated successfully
albums/userpics/10001/thumb_14~0.JPG updated successfully
ERROR creating: albums/userpics/10001/thumb_13~0.JPG
..."
Extract of run 2: "...ERROR creating: albums/userpics/10001/thumb_16~0.JPG
albums/userpics/10001/thumb_15~0.jpg updated successfully
albums/userpics/10001/thumb_14~0.JPG updated successfully
albums/userpics/10001/thumb_13~0.JPG updated successfully
ERROR creating: albums/userpics/10001/thumb_12~0.JPG
..."
As you can see the update was good for 14~0.JPG and 13~0.JPG, which I uploaded step by step for testing your suggestions.
If I ran the tool for all Albums, would it show me a list of all missing pictures??? It would be easier for me to identify those, than seeking for them through every album. Or do you see another way to repair quicker all missing pictures? I am afraid of destruction in anyway.
Thanks in advance