Take a look at the Attachment Manager submodule of the Python API.
In particular, there is an update function. Using this requires you knowing the attachment ID of the file in question. It's possible to use the search function to get a list of all attachments in the layer, then using the values in that list, you could iteratively download, process, and update the files that way.
I don't know what your processes look like that you mention in your post, but if you have a way of maintaining the list of attachment IDs associated with each file, perhaps by exporting the search results, you should be able to use that when updating the files.
Can you elaborate on the existing process you have in place?
- Josh Carlson
Kendall County GIS