The app's limitations depend solely on the Salesforce org limits since it is a 100% force.com app.
The app does not integrate or connect with any external server or service.
According to the governor limit set by Salesforce, the maximum number of records that can be retrieved using SOQL queries is 50,000. This limitation applies to the Mass File Download app's ability to query and search Object Records, Files, and Attachments.
Suppose your org has more than 50,000 records. In that case, you must apply filters or use SOQL queries based on criteria such as CreatedDate, Modified Date, or any other standard/custom field values to narrow the search results and keep them within the 50,000 limits for the first iteration of downloading files. In the next iteration, specify another set of filters to retrieve the next 50,000 and so on.
By doing that, you can ensure the app functions within the permitted boundaries and still helps you download all the files.