What you show is actually quite reassuring: you obtain similar source maps if you change a bit the source space.
The surface that is used to display the MNE results when you double-click on them is really the source space that is used for estimating the sources. You should not fear that Brainstorm uses some cached version of the cortex surface.
If you look at inverse results computed from these forward models: unless all the signal observed in EEG is identified as originated from the area you removed from the cortex surface, you should not expect major differences in the two versions, especially if you look at the flattened unconstrained source estimation in a 3D figure.
However, the results cannot be strictly equal. If you want to observe this: create a scout with one vertex only in the two versions of the cortex (the same one), set the scout function to "All", extract the scout time series for both source files, concatenate the two files and display the results, or plot the signals from Matlab: they should have the same shape but if you zoom in, they should not overlap perfectly.