sites/subDomain/libraries doesn't load the library files
I think you would want to keep the imageFlow library itself in the sites/all/libraries folder, then to adjust the images for each site, modify your theme to override the default css and images of the imageFlow library. You could do this by copying the imageflow.css stylesheet into your theme, including it, then modifying it to point to custom images instead of the imageflow default images.

This would be a little bit more standard approach than changing the imageFlow source files.