According to the log Renoise just “vanished” a few times for you. Did you got any error messages for that? There’s nothing in the logs. Maybe it’s directly or indirectly caused by some of the bridged plugins. Not saying it’s not Renoise’s fault but it only seems to happen after loading and unloading a lot of plugins.
Destroyed the preferences indeed just means that the “object” is down. It’s not deleting the file.
If you still get this problem when simply launching Renoise, changing the keymaps, then shutting down Renoise, then this also could be caused by your anti virus software. Some AV tools may treat the keymappings.xml file as ‘suspicious’ because of the linked style sheet.
Which anti virus software are you using?