The way contacts are logged is as follows:
HRD Logbook has to be running in order for QSO Relay to be able to add a QSO. The only method supported for writing QSOs into HRD Logbook is via a command line interface (CLI) that requires that HRD Logbook to be running.
If QSO Relay can't get a response from the HRD Logbook CLI, it caches the contact, and the next time you Synchronise Databases in QSO Relay, it will try multiple times to log the contact. So, if you experience a temporary outage of HRD Logbook, your QSOs will not be lost. Simply restart HRD Logbook, perform a Synchronise Database operation, and QSO Relay will try again to add any cached contacts into HRD Logbook. However, this is a costly exercise - it can take many seconds to process each cached contact. So in the normal course of events, you should always have HRD Logbook running.
The ADIF file is only used by QSO Relay to provide a complete extract from HRD Logbook for JTAlert to read duing its Scan Log and Update process to update your wanted alerts requirements.