This is probably only a one-timer for a user, but technically it is a bug.
Problem
The "Folder" and "Attachments folder" setup is not respected if updated after the sync.
Replication
I let Omnivore Plugin sync the notes to the default folder (just to test it out).
After that, I updated the folders in the settings. Then, during the next sync, this setup was not respected.
Desired behavior
Sync should respect the updated settings.
Resolution
I've currently resolved it by uninstalling and installing the plugin again and settings up the correct folders in the General Settings before the actual 1st sync.
This is probably only a one-timer for a user, but technically it is a bug.
Problem
The "Folder" and "Attachments folder" setup is not respected if updated after the sync.
Replication
I let Omnivore Plugin sync the notes to the default folder (just to test it out). After that, I updated the folders in the settings. Then, during the next sync, this setup was not respected.
Desired behavior
Sync should respect the updated settings.
Resolution
I've currently resolved it by uninstalling and installing the plugin again and settings up the correct folders in the General Settings before the actual 1st sync.