Hmm. That's interesting. I'm guessing that happened because:a) it's Atlas flex track, not MicroEngineering; and/orb) it's not glued down. I've cut several gaps in the helixes without issue. So I guess the answer is to use insulated rail joiners in the loops instead?
Filling the gap with as thick styrene as your cut should also avoid this problem. As would spiking on either side before cutting.