Write Running Config?

We have a 1000A with ~4000 tunnels terminating on it. We reboot it about once a month to keep memory usage from going through the roof, from time to time, we have seen it drop its most recent config changes. Typically, when changes are made to the config, FortiGate devices generally write it to the startup config immediately, I believe. However, it seems like our 1000A is failing to do this (probably due to the size of the config). Is there a command that can be used to force it to write the changes? Thanks,