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Will it be an update that replaces the current RiotX on my phone, or will I have to download it as a separate app?

It will replace the current Riot Android App. So if you are an early adopter of RiotX you will need to download the main app.

edit: commented before reading TFA, it'll probably be a new app.

Same for F-droid? I suppose I'll need to be testing the migration process again..