[Klojum]

Thanks. But rescrapeing would mean I'd lose the previous library

No. You keep the same library. You move the videos to their new location. You tell Kodi to clean the video library, and then you update the video library. That should do it.
I said rescraping, I meant updating. Sorry.

Or in other words, after loading my movies from one drive, if I want to scrape my documentaries from another drive, I'd lose the movies, isn't it ?

No, Kodi has no content provider for 'documentaries', afaik. It's either movies, music videos or tv shows, it all goes into 1 video database.

Any smart ways to bypass that and allow simultaneous media input from two different drives ?

Already explained. You can add several paths to a video source. You can also add another separate video source for documentaries, but you still need to identify them as movies or tv shows when choosing the content/provider.