The idea was correct,
but you should not LOAD the points, you should pick up the file you saved using the menu on the left (menu item: choose a real file).
Save/Load options use an internal format. While saving a subselection of points from scatter plots writes values in a SxL matrix (the common sw format). Make sure to choose also a parameter for the Color axis in scatter-plots: this will save such parameter in the SxL matrix (instead of just ones). The APS module may use the value for optimization purposes.
About long time:
a. check that the process is parallelized. sometimes matlab takes time to start the pool and the process starts in serial way
b. long time may be taken if u are processing totally noisy points or if NaNs are in the data (in this second case, u get messages).
I believe that after a few cases u will understand which options to choose to better choose points and limit the time…