As long as the batteries stay in range. You, of course, would not want a 50v and a 39v battery. They both need to be designed for the same motor voltage.
I suppose there is the question running internal down to cutoff, then adding external. The computer only knows about one virtual battery, it sees the new fully charged external and continues to allow full power. The essentially empty internal is not "cutoff" or throttled down. Will it damage the internal once the external also begins to get exhausted but not enough to kick in the limiter. Without ideal diodes they would equalize and act as one battery. But with ideal diodes to prevent that.... I am not sure what happens.
With the switch controller it switches out the low voltage battery and lets the new battery take all the load. The trouble with the switches is that they are big and hard to fit in the frame and two they don't handle charging so you have to have separate lines to charge independently and the charge lines to the battery can't be connected to the output of the battery.