How do you normally operate the ladder line?
Using a balun or via an antenna tuner that provides balanced output?
In case you use a balun simply connect the nanoVNA to the balun and measure.
When using an antenna tuner disable all "tuning" and use the tuner as a pure balun.
Without a balun (in case your receiver has something buildin) your proposed approach will work but be aware the ladder line impedance is high compare to 50ohm
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