One gotcha to watch for will be file name clashes. We have an option to handle that ("keep original and increment name"), but that relies on the files being where we expect them to be. So you'll need to handle that yourself.
I would also suggest updating the table row Fabrik updated, to remove the path data, so Fabrik doesn't get its undies in a bundle expecting to find files which aren't there. Actually, given that this is Ajax uploading, which creates a separate table to store the one-to-many data, you'll probably want to remove the rows in that table entirely.
BTW, just a suggestion, but have you considered a private Amazon s3 bucket for this? I think you could achieve the desired results, but using S3 rather than local storage may not meet your requirements.