Loose or perhaps just undersize phase wire is the likely cause, though it could be controller or halls related.
I had a wire that intermittently rubbed on the tire only when the forks were compressed. It rubbed through one phase wire, cutting all but one strand on the green wire. Ran great at low speed, or no load. Take it out and put a load on it, and stutters. It was hard to spot, not looking like it rubbed when I was not on the bike, bouncing the shocks.
So look hard at all wiring, plugs, contacts that may be backed out, etc as the step one of any troubleshoot.
THE LIPO RULES. NEVER ABOVE 4.3V NEVER BELOW 2.7V DON'T PUNCTURE
Ideal charging /discharging range for Lipo, 3.65v minimum 4.1v maximum
See battery technology section, FAQ thread at the top of the page for lipo noob info.