Interesting... I hadn't thought about that yet.
I just had a look at the events structure in the savegame and it seems the flags are also stored among the events (as a special first event without any actions or triggers). So, yes, that means they also get deleted.
You shouldn't really need Delevent, though, with ToT having such a large amount of memory available for events... Or do you have so many events that it won't even fit inside 100kB (that is, in memory, not the events.txt file)?