I selected a 3 day per week journey (Thursday, Saturday, Sunday). Because I had free time yesterday (Tuesday ) I did one proposed weekly workout (charon) which was not personalized. Today (Wednesday)a journey workout was popped up (Persephone) in order to complete ot, but it was not scheduled. Do I have to complete it? It will affect the journey path? How can I disregard it?
Sounds strange, as if you might have accidentally “started” the session that might have been scheduled for tomorrow.
You don’t have to do it 
You can just do it tomorrow-but be aware that you might need to scroll back to today (i.e.Wednesday) in the weekly calendar if it has indeed been moved today.
Won’t affect your Journey negatively in anyway. You should feel enabled to do your training when it suits you. Hopefully the below helps give some more detail 
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Hi Ben. Thanks for the advice.
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No worries, we’re all here to help