IIRC, if a monk knows the correct voodoo, it's possible to edit your own rootnodes.

I've got a few suggestions, I'm not saying I've got the answers, nor if it's possible to do any of this within Everything:

• Remove the ability to edit your own root nodes for normal monks.

Personally I don't like my own suggestion, since it would only prevent people updating their own nodes when it is really necessary and create more work for the editors.

• Make it clear to all monks that deleted root nodes will be recovered from backups (and access for that monk to alter them removed?)

Also not ideal - removing posts is generally a Bad Idea, however people should probably be allowed to retract their own comments. Free Speech (or no Speech).
Maybe the option of removing the ability to edit your own root nodes should be reserved for only those users that seem to be removing their own nodes.

• Place a limit on the amount a root node can be altered - i.e. refuse to commit if the user deletes more than 20% of the post

Probably more trouble than it's worth and could be easily circumvented. Instead of empty root nodes, we'd end up with noise to make up the required characters.

• Remove edit permissions from a monk for a period of time if any rootnode is edited or truncated.

This might just stop any large-scale removal of nodes by a disgruntled monk.

As far I see it, there isn't a simple solution to the vanishing rootnode problem.
Something should probably be done, however, as a reasonable number of missing root nodes would impact the Monastery as a whole.

Cheers,

BazB