This is my take on the subject.
Thanks for your input Henu!I agree on many things here, and recommend people to check this video out.
One thing that is also really crucial is that in case of backupping things, it's really useful also to mix with audio: in that way, in case you need to go back to the mix backups later, you can still be 100% sure the audio sounds as intended.
I personally have two methods, depending on the project size. When working with multiple songs in the same project (a.k.a same mix settings for all tracks) I always have two separate projects when working with midi- one is the "record project", which has the midi data and VST's and the other is the "mix project" where I always import the tracks as audio.
In case I work with only one song, I render everything "in- place" in Cubase, disable the midi track and start mixing with the audio files. If I need to change something for some reason (let's say that I can't get a particular sound to sit in the mix so I need to use another patch), I just enable the midi track, do the tweaks, render again and then disable.
It's also crucial if you have more going on than just a couple of Kontakt instances in your project. Most of my songs also contain recorded audio so that's also another reason I like to mix everything as audio.
Right now I'm working with a project that has placeholder midis for demo tracks and all the vocal and instrument takes are recorded on top of those to-be-replaced placeholder tracks. After the recordings, we can start tweaking the previous quick midi tracks to fit the newly recorded audio, export everything out into the mix project, backup the "record projects" and pretend they never existed.