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What do you mean by that? What exactly is your technique to fill in the in between "NaN" values? When I put a beginning value and end value and finish sketch, the "NaN" values for the middle vertices stays "NaN". Do you have a trick to "fill in" those values with the correct geometrically derived lengths?
I can use calibration points, but those don't work on complex lines ("Y" shaped lines for example). Any help would be appreciated.
What you are describing are multi-part lines. You will have to decide when creating an LRS how to handle both directions there are a few options available (I believe you want to preserve overlapping segments).
Creating a complex (looping) route—Help | ArcGIS Desktop
Complex routes
The process of creating a complex route is very similar to that of creating a simple route. The only real difference is that you must build a complex route in pieces. Once the pieces are created, they can be merged.
Take note that in creating a complex (looping) route in the task, care has been taken to set the measures appropriately for each of the two halves of the route that are eventually merged. If this is not possible in your situation, you can still merge the pieces. Then at a later time, the measure values can be reset.
Personally I avoid complex dynamic segmentation, I have ALWAYS found a way to create a simple route even under complex situations (Sometimes you got to think out of the box!)