Mavericks not "seeing" files on external hdd

This has to be the single weirdest thing I've ever experienced on any Mac I've owned.
I have an external hdd that contains all my pictures sorted by year, followed by a folder for the raw images extracted from my iPhone using Image Capture. This is done on my iMac and I've been doing it this way for years.
Today, I freed up some much needed space on my iPhone using the above method. When I deleted the images from my Camera Roll on my iPhone, I went into the external hdd and saw that the files I just literally transfered were gone! I checked the trash, other folders and even the desktop and they were gone...simply disapperared. Clicking into a random year showed no subfolders, consequently: no files.
Frantic, I unplugged the external hdd and plugged it into my Macbook Air (not running Mavericks just yet). The files from the aforementioned random year were actually all there, as well as some root folders containing iPhone pictures I backed up a few weeks ago. It even had the photos i transfered off my wife's phone prior to working on my own. But the folder that shows my photos were still not there.
I am currently running a diagnostic software for data recovery. There is no iCloud backup as of last night (most recent was two days ago). Not a photostream person so that's not turned on. I was able to get many of the photos from the Google Plus iPhone app.
My question is: what gives? How does Mavericks show an empty folder but my Macbook Air shows files? I just used this external hdd on my iMac the other day and those files were there. There is no hidden files option or anything...no preferences have been changed on the computer. Why is this happening and can I get my "deleted" data back? For the life of me I cannot understand some features in Mavericks...but this one erks me.

Interesting that no files show when plugged into the USB port, drive looks empty with the exception of the space remaining. Folder structures show when plugged into firewire 400. The drive has an external power supply.

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Hi all I am a noob to MAC so here goes.
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Finally, I have read stuff about how the HDD is formatted. Could it be the reason?
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Hello everyone,
Hallo Zusammen,
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Es wäre großartig wenn mir jemand helfen könnte!
Thanks
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Donwload Link: Downloads - RED Digital Cinema
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best regards,
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Mavericks not "seeing" files on external hdd

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