I hardly ever use hot swap, and more often than not, stale saved sessions get in my way when debugging.
I use hotswap constantly and get annoyed when I have to navigate through stateful apps again :)
So these two points wouldn't bother me. Anyway, when you get round to implementing the "redeploy on save" feature, if you provide a configurable timeout (which may be infinite), then the users can decide on their own how to work with the plugin.
Which timeout exactly do you mean here ?