Scenario 1, One Document Per Account
This occurs when one account has multiple entries in a query, but we’ve selected that we should download One Document Per Account on Step 2 when we run the letters (see below).
Step 2 of the Document Generator 

 For example, if we query for all of the donations to a specific Fund, some donors may have given to that fund multiple times. When we select One Document Per Account, these donors will receive one document to summarize their giving, which lowers the total number of documents we will receive from the download.
Summary Page for Multiple Transactions

Scenario 2, Auto-Mail
The number of documents you will receive can also be affected by the number of documents that will be auto-mailed. On Step 4, we can indicate that anyone who has an email address on their Personas page should receive their letter via email, rather than printing the letter (see below).
Step 4 of the Document Generator

When we select this option, we will not receive a downloaded version of the letter if the recipient has an email address on file. Thus, we will receive fewer documents in the download than the total number in the query.
Summary Page for Auto-Mail
Please note that we can run into a combination of these scenarios. For example, if we use a query that searches for all donations to a specific Fund (some donors gave multiple times to the same Fund), and we also selected the Auto-Mail option, this would result in fewer documents in the final download.
Summary Page for Multiple Transactions and Auto-Mail