While Salesforce requires Multi-Factor Authentication (MFA) for all users, this requirement does not apply to system integration login types via the API, such as those performing S-Doc Job operations. Setting the Session Security Level Required at Login to "High Assurance" for profiles performing S-Doc Job operations restricts the asynchronous processing performed by S-Docs Jobs and causes them to fail or produce corrupted files. (See "Considerations" for the section "Is MFA required for my integration users?" in the article linked.)
To avoid this, navigate to the Setup menu, type "Profiles" into the QuickFind bar, and click Profiles in the dropdown menu. Then, click Edit next to the appropriate profile name.
Scroll down to the Session Settings section, and ensure the Session Security Level Required at Login is set to None (not High Assurance).
Setting Up MFA in Session Settings
Setting up MFA in Setup > Security > Session Settings (as shown below) will not impact S-Docs.