No there is no way to flatten the directory structure
Take a look at How to upload product images via FTP instead of using the Magento UI?
The structure is fairly simple. For product ABC1234, the images for
that product would be placed in the
The first folder in the product folder is the first character of the
product number. The subfolder under that is the second character of
the product number.
So for product DEF6789, the structure would be:
Assuming that there is some logic to your file and they have the same name as the existing image in magento then you could either
Create a bash script to move them to the correct directory (assuming that the image name is also the product name)
Create a script that load your product collection the programmatically update the product see Magento programmatically add product image
Be careful to make backups of your directory structure before running these scripts, as you can severely mess up your files if you are not knowledgeable and careful.