Normal Factorio behavior saves all updates to _autosave files. This can be a detriment because if your server ever crashes for some reason your primary save will not be updated with all your latest changes. Upon reboot, the server will load your primary save you named which may be days or even weeks behind in progress and then overwrite the _autosaves as the autosave time period is triggered. Unforutalty there isn't much we can do about this behavior but we do have a workaround on our platform that can protect you from lost progress.
We recommend the following command setup in our panels scheduler.
Day of the week: *
Day of Month: *
Hour of Day: 0,12
Minute of Hour: 0
Then set up the "Send Command" payload to be "/server-save".
This will force Factorio to save your server to its main save file twice a day.