Inability to Save

I have a serious issue, and this has happened multiple times.

Whenever the server is closed, it is reverted to a specific time beforehand, no matter what is done before the server is saved and stopped.

Is there any way to prevent this? /save-all doesn't work, and the server saves multiple times every 10 minutes.

Would using WorldEdit have serious effects on save? Because we made a cool pvp area using it.