Coming through AUX, there's an extra fuse.
Coming through charger terminals you bypass that fuse, but you still go through main contactor.
Main contactor is programmed to disconnect (open) if you exceed safe charging rate, if you exceed voltage, or if battery gets too hot. Very effective battery protection, imho.
I doubt you damaged the battery with aftermarket charging. But an unscrupulous or uninformed dealer may make that claim to avoid work, avoid analysis, etc. I'd remove anything aftermarket that might get in the way (of proper analysis). Zero will see the rapid charging in the logs, regardless; you certainly would not want to lie about it.
I *do* charge via controller terminals, up to 1C, with aftermarket charging. Indeed, when my onboard charger failed, I charged *only* with the diginow units for several months. And I have contacted zero about warranty claims, had no issues. But I have not had sufficient battery degradation to file a claim on the battery. I thought I did, for a bit, but it turned out it was not the battery that was poor, but rather the measurement of the current. They've offered to replace the MBB but the bike runs great otherwise, so I just ignore the inaccurate % full. But no, I have not had an issue with Zero honoring warranty.