"Workflow" is a term of art in business software that typically encodes into software what would have been the movement of paper around an office in the past.
In an old paper office, documents would go into people's inboxes for decision making, and would be forwarded to someone else when done. Think of customer service taking a report from a customer (this is the inbox for Customer Support), turning that into an entry in an internal bug database (the inbox for a developer), and then into a code fix up for review (the inbox for a different developer), and so on. This is a workflow. Work literally flows from one person to another throughout the organization.
Where integration between different software systems occurs, there's a spectrum of choices, from humans poking data into UIs through to direct API calls. One of the cheaper automated-yet-ad-hoc integrations is a script which FTPs files into well-known directories, often with semantically significant directory and file name conventions (e.g. dates or company codes). The receiving system polls the FTP location for new data (frequently CSV files), often using regexes or other techniques to extract metadata from filenames (since CSV doesn't really support non-repeating metadata).
So FTP workflows is an ad-hoc workflow integration using FTP to connect two different software systems, replicating what would have been done by paper 20 years ago.