I have a system that is currently running Asterisk 1.6.2.6 (old I know) and it’s been running for us just fine for a while but recently I was getting input/output errors and errors when trying to delete files so I was thinking the flash drive was failing. I shut the system down and brought it back up again which forced a disk check and while that seems to have cleared up the errors I was having the one thing I noticed is that it seems to have deleted the voice mail boxes. I can save new voice mail messages and they get delivered to the user just fine but when I perform a shutdown -r now the voice mail boxes get deleted again. Calling the extension recreates the voicemail box but doing a system restart a seems to erase the voice mail boxes every time.
Asterisk itself doesn’t delete the folders unless emailing with the option to delete the message as part of the process. This is likely happening somewhere outside of it.