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I ran into a similar problem when building my media library with large movie files, that would take 30 seconds to a minute per movie to add to Calibre. I found a way to move the files instead of copying them. The trick is to use a placeholder file.
WARNING! (Standard disclaimer about modifying files in your Calibre library. If you don't know what you're doing or can't trust yourself to perform these steps exactly, DON"T TRY THIS!)
First, I created a small text file on my hard drive (not in the library path). Then, for each movie file, I performed the following steps:
1. Copy the name of the real movie file and overwrite the name of the text file. IMPORTANT: Include the file extension.
2. Add the renamed text file to Calibre. This should be almost instantaneous because you're only copying a few bytes. Note that, at least for formats Calibre doesn't recognize, it doesn't care whether the file is valid. It won't nag you about the file not being a valid .mp4 file or whatever.
3. Open the containing folder for this "dummy" movie file.
4. Copy the name of the file and paste to overwrite the file name of the real movie file.
5. Drag and drop the real movie file into the library folder, overwriting the dummy file. This should also be instantaneous because you're moving instead of copying the file. Important Note: If it doesn't ask you if you want to overwrite the existing file, stop what you're doing and figure out what went wrong RIGHT NOW. Move the real movie file back out of the library and repeat steps 4 and 5.
If you're careful, it should work fine. The only drawback of this method is that the file size is reported wrong in Calibre, and I haven't found a way to fix it. If an inaccurate file size bothers you, don't use this method.
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