Is this product suitable for this workflow?

Hi,

Thanks for contacting us here about this extension.

1. Customer logs in
   
2. Customer securely uploads file, usually PDF but potentially another format like *.indd or *.zip. I am notified. Only the customer and I can view this file
   

Yes, sure. With the unusual format, you can add new file types at Options > Allowed extensions.

3. I download the file and replace it with another file. Only the customer can view/download the replacement file

You can set the permission for users to view and download on frontend.
For more details: https://www.joomunited.com/documentation/dropfiles-documentation#toc-4-3-acl-file-permission

4. Customer downloads the replacement file. I am notified/their download is tracked

Yes, we have that feature. An email will be sent to owner/admin if a file is downloaded.
For more information: https://www.joomunited.com/documentation/dropfiles-documentation#toc-2-7-email-notifications

5. Customer can see their full file download history

This feature is impossible presently.

Hope it helps!
Cheers,