On the system that I’ve been testing I have had the logging on long enough to catch the delete event.
Delete events:
2019-03-23 20:07:19 -05 - [Information-Duplicati.Library.Main.Operation.DeleteHandler:RetentionPolicy-StartCheck]: Start checking if backups can be removed
2019-03-23 20:07:19 -05 - [Information-Duplicati.Library.Main.Operation.DeleteHandler:RetentionPolicy-FramesAndIntervals]: Time frames and intervals pairs: 7.00:00:00 / 1.00:00:00, 28.00:00:00 / 7.00:00:00, 365.00:00:00 / 31.00:00:00
2019-03-23 20:07:19 -05 - [Information-Duplicati.Library.Main.Operation.DeleteHandler:RetentionPolicy-BackupList]: Backups to consider: 3/22/2019 7:00:00 PM, 3/21/2019 7:13:53 PM, 3/19/2019 8:14:29 PM, 3/18/2019 8:12:58 PM, 3/17/2019 7:27:47 PM, 3/15/2019 8:55:48 PM, 3/12/2019 7:16:04 PM, 3/4/2019 6:36:15 PM, 2/24/2019 9:55:06 AM, 2/15/2019 6:26:26 PM, 1/14/2019 6:23:53 PM, 12/6/2018 7:31:18 PM, 10/11/2018 7:51:40 PM, 9/9/2018 9:46:01 PM, 8/9/2018 7:22:39 PM, 7/8/2018 8:21:36 PM
2019-03-23 20:07:19 -05 - [Information-Duplicati.Library.Main.Operation.DeleteHandler:RetentionPolicy-BackupsToDelete]: Backups outside of all time frames and thus getting deleted:
2019-03-23 20:07:19 -05 - [Information-Duplicati.Library.Main.Operation.DeleteHandler:RetentionPolicy-AllBackupsToDelete]: All backups to delete: 3/22/2019 7:00:00 PM, 3/15/2019 8:55:48 PM
...
2019-03-23 20:09:06 -05 - [Information-Duplicati.Library.Main.Database.LocalDeleteDatabase-CompactReason]: Compacting because there are 51.84 MB in small volumes and the volume size is 50.00 MB
...
2019-03-24 03:01:39 -05 - [Information-Duplicati.Library.Main.BasicResults-BackendEvent]: Backend event: Delete - Started: duplicati-id194d476d9c041b0a43dd0221ee249e3.dindex.zip.aes (133.26 KB)
2019-03-24 03:01:41 -05 - [Information-Duplicati.Library.Main.BasicResults-BackendEvent]: Backend event: Delete - Completed: duplicati-id194d476d9c041b0a43dd0221ee249e3.dindex.zip.aes (133.26 KB)
2019-03-24 03:01:35 -05 - [Information-Duplicati.Library.Main.BasicResults-BackendEvent]: Backend event: Delete - Started: duplicati-i8046624c02fa40889cf63b96b0c76660.dindex.zip.aes (80.58 KB)
2019-03-24 03:01:37 -05 - [Information-Duplicati.Library.Main.BasicResults-BackendEvent]: Backend event: Delete - Completed: duplicati-i8046624c02fa40889cf63b96b0c76660.dindex.zip.aes (80.58 KB)
Missing file reports
2019-03-24 19:28:53 -05 - [Warning-Duplicati.Library.Main.Operation.FilelistProcessor-MissingFile]: Missing file: duplicati-id194d476d9c041b0a43dd0221ee249e3.dindex.zip.aes
2019-03-24 19:28:53 -05 - [Warning-Duplicati.Library.Main.Operation.FilelistProcessor-MissingFile]: Missing file: duplicati-i8046624c02fa40889cf63b96b0c76660.dindex.zip.aes
It looks to me like whatever logic is compacting small volumes is doing something wrong.