Hi wingman, I wonder if you could be a bit clearer?

Are you using the "overnight" feature where this suggests stops based on the distance (or time) supplied in your settings? 

And are you doing this on the app or on the website?

Or is there some other way that a preferred daily distance comes into play? (It's always interesting to find out how others use CT)

I've just created two routes on the website, suggesting overnights based on  using different "distances per day" and playing around on one route doesn't seem to affect the other - unless I go right back and recalculate the route. That's in the case where the first route has a daily distance of 80, the second at 160.

IF you are talking about "Overnight stops" I can think of two suggestions:

Plan your first route and save it using the "split into multiple days" option. 

Change your settings and start planning Trip 2

Or

Leave the settings for the longest "daily distance".

Plan the "short daily distance" route by adding "Overnight stops" manually. They can be added in the same way as a viapoint (and existing ones removed in the same manner),

I repeat, this was done on the website, it's possible that the app will behave differently.