Yes, by all means turn your converter off. Remove the ground lead from the battery first, then the positive.
If you want to turn the converter back on (Parallax says its OK)first insulate the positive battery lead. Wrap it up in a plastic bag and tape it so there is no possible way it can touch the frame. Use multiple layers of plastic so that a sharp point or wire can't penetrate the wrap. Turn the converter back off again before you install the new battery.
Battery in place, the converter should be maintaing 13.8 volts. I presume you have checked to see that this is the case???
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