But after redoing the plot, you pressed again the plot to be a stem plot? Because I assume that after redoing plot the plot is not a stem plot in your shown image
As Luc already noted - the problem is the number of points you demand to be plotted. In your last example you demand 6827 points to be plotted, but Prime only allows up to 4999. Not sure if this limit is documented somewhere (EDIT: It is partially - see my note at the end).
If you demand 5000 or more points to be plotted, Prime will automatically choose the full dot as its shape (Symbol) and the smallest thickness and will not allow you to change that. In case of a Stem Trace you even get that error without an error message which sure should not happen and is a bug.
BTW, you get the same buggy result if you try to plot a vector with more than 4999 entries over another one of the same size.
EDIT: Just found this in the depths of the help pages:
Actually it should read 4999 instead of 5000 and should be clearer about the exact limitations. And of course the behaviour with the Stem Trace still must be considered a bug.
This idea with splitting points when someone wants to display more than 4999points on the graph is ok only when we have not such more points to display from beginning, like for example If we have 8000 points then we can split into 4999 points then the rest of remaining points, but when we have 50 000, or 100 000 points or more then will be not at hand to split so many points into so many intervals of maximum 4999 points.
5000 points allowed for graph display is very limited. If this limitation was 50 000 points or 100 000 points or greater then it would have been way more better.