Hello André,
I don't know if you managed to solve it, but here is my solution to workaround this issue.
I created a button to open colormapeditor. The button callback uses copyUIAxes. Basically, the current plot is copied as a "normal" figure (which is hidden during all process). app.fig = figure;
app.fig.Visible = 'off';
copyUIAxes(app.UIAxes,app.fig);
colormap(app.fig,originalcolormap);
colormapeditor;
I didn't find a good way to update the plot's colormap once the colormapeditor is closed... I tried using a "while" but then the colormapeditor was impossible to acess. However, I have a button "plot". So basically, the user has to click on "plot" button so the colormap updates. I created a private function to return the final colormap from the figure, like this:
figaxes = app.fig.CurrentAxes;
app.currCM = get(figaxes,'colormap');
In my case, the user also has the option to choose from MATLAB's colormaps - a drop down menu. So basically I use "clock" to save the time that the colormap was changed (for both colormapeditor button callback and drop down menu callback) and when the user clicks "plot", the times are compared and the most recent is chosen.
Sadly, I could not find a way to update the plots with the new colormap automatically.