IPhone photo/video library glitch - wrong file extensions, name shift, lost files etc [LONG story - sorry]

Question

I have a 5s running 7.0.4. and my computer is running Windows 8.1.
We had a baby and my phone filled up fast with pictures and videos, so I decided to offload them onto my PC. I connected my phone to the usb port, and directly copied from the DCIM folder to my hard drive.
Something happened during the first attempt, and the process was interrupted. So I went into each of the sub folders, and selected all files, and started the copy process again. I told the computer to skip any existing files.
So all the file counts matched in each folder, and I figured it was safe to start deleting from my iPhone.
On my hard drive, I separated all the MOV files into my Videos folder. But in Windows Explorer, the thumbnail view showed several MOV files with no thumbnail - just the generic icon.
As I sorted my photos into various folders, I also noticed a lot of generic icons instead of thumbnails for the JPGs. I started to feel concerned that my files had become corrupt during the transfer. But then I noticed a PNG file that was a few hundred megabytes. This was odd, so I added the MOV extension to it. Sure enough, it was a video with the wrong extension.
I renamed every PNG and JPG file that had no thumbnail to add the MOV extension. Every one was a video with the wrong file extension.
Then I went to the video folder, and all the MOV files that had the generic icon were actually JPG files.
Well I was just happy to see that the files were not corrupt.
One more time before I deleted things from my iPhone, I did a spot check to see that the largest videos were on my hard drive. I found a few videos that were not copied over, despite the file counts having been accurate. So I copied the videos again, and compared file sizes and date/times when there was an overwrite prompt. Most were matches, but several were the same file name with different sizes and dates.
I didn't know what was going on, but I just wanted to get the files on my computer. So I renamed my local copy where there was a name collision, and copied the videos. I deleted the videos from my phone as I went along.
I felt pretty confident that I had all the files copied now, so I began mass deleting my photos.
I went to the Photos app on the phone, and watched the thousands of pictures disappear, and the glorious free space grow on my phone.
But wait... there was still 1 video in the Photos app. I thought I had gotten all the MOV files off the phone...
I have a photo info app installed, so I was able to see the file name of the video. I searched for that file name in the DCIM subfolders, but the folder that had that series of files (the IMG_3000-3999 files) listed the files with that particular video skipped. It was clearly still on my phone, because I could play it.
Then I noticed it was a 45 minute long video of my baby. About 5 GB. So I figured it must be due to the file size that it wasn't visible from explorer. (Can't explain why that would be, but M$ keeps changing crap too. I never freaking know what to expect from them either.)
After having deleted all the jpg, png and mov files from the DCIM folder, there were still about 26 files in my camera roll on the iPhone. And I could still view the video.
I decided I wasn't concerned about the photos, I just wanted to figure out how to get the video onto my computer.
So I selected all the photos in the photo app (skipping the 1 remaining video) and tapped the trash can.
Poof! One item remained, and it was one of the garbage photos. My video is GONE! ^#@*&#($^@Q&%( And no, I didn't fat-finger it. I was very careful to select the correct thumbnails.
Looking back, I know that I should have just started the entire file copy process from scratch when funny stuff started happening like mismatched file names. But I am a sleep-deprived new mom and just wasn't thinking clearly. It would be nice if I could have used my file/directory compare program to check the iPhone against my laptop, but it is not compatible with devices, only removable drives.
And no, I don't use iTunes. I stopped using iTunes years ago when it would randomly decide to delete contacts from my phone just because they didn't exist on my computer or some sh-- like that. I have always just manually synced all my stuff and have never had an issue like this. To say I am sad to lose that video is an understatement.
I googled "iPhone undelete" and "iPhone data recovery" and downloaded a trial for one of the likely candidates. It turned up a bunch of garbage, but not my video.
Anyways... I am wondering if anyone else has experienced this type of scenario? Has anybody identified what could cause this to happen? I would like to avoid this in the future. (I will avoid this type of loss, because I know now what I could have done differently to be more careful. But it would be nice if I didn't have to get all neurotic about checking 60GB of photos/videos side by side each time I copy them to my computer...)
I have seen other threads on the forum here regarding corrupted libraries and such, but I am not sure this is the same thing.
One suspicion I have is that it might have to do with the iPhoto app being installed on the phone. I can't articulate why I think that is worth considering. But when I looked at my Video folder, I ended up with many duplicate videos, and all the duplicated videos' file names were 2 numbers apart. As if all the file names got shifted at some point. Very strange.
Thanks for listening to my rant. If anybody has an idea, I am interested. If anybody else has lost precious memories due to this, we should talk. If it is a widespread problem, maybe we can all get together and pound down Apple's door?
As an aside: Why am I unable to select Apple Support Community to post this question to?

Answer 1

In my case number of weird things happen whenever I try to copy pictures/videos from my iPhone from direct USB...
1. JPG files are wrongly named as MOV and vice versa.
2. I copy only folders but in addition files with no extension are copied in the main folder, very strange.
3. Whenever I open one of the folders, strange icons like this () start appearing which cannot be copied even.
Unfortunately I used to delete a lot of files with wrong extensions in the past because I never new they could be fixed.
Apple should answer this!
Note: I am using Windows 8.1 and use a direct USB cable without iTunes to copy the media files directly from My Computer.