Error 'Could not save the settings file' relates only to agents internal settings and doesn't concern synced files.
Each agent keeps its settings in a special file inside its storage folder - sync.dat
Current setting are kept in sync.dat. Periodically Agent backups it: sync.dat file is renamed to sync.dat old and agent's current settings are written to sync.dat file again*.
Periodically - means every 10 minutes by default and at exiting agent.
* to ensure correct writing of current settings, they are written to sync.dat new file, which is renamed into sync.dat. This operation takes less than a second, but prevents loosing settings.
The error message appears when any of the above mentioned operations failed. As a symptom you'll also see sync.dat.new file in storage folder.
Possible reasons and fixes are:
1) Agent was not shut down correctly, for example, at poweroff. Even though it will attempt to restore settings from sync.dat.old, this one may also be corrupted.
Possible solution: Stop the agent. Remove sync.dat file and start the agent.
2) Agent's access permission changed and now it has no write access to storage folder.
Possible solution: in process list check under which user agent runs and ensure that this user has rw access to its storage.
3) Improper value in its settings. This usually happens when editing agent's or MC's config manually and either mistyping or misconfiguring anything in there.
Possbile solution: Stop the agent. Remove sync.dat file and start the agent.