It ought to, but it would be worth checking with Cyclepoint.
A charger for a lithium battery generally just supplies a voltage, and the charging is controlled by a circuit in the battery - BMS or Battery Management System. So in theory any 36V Li-Ion charger should work with any Li-Ion battery.
The reason I suggest checking is that there are two or three types of Lithium battery technology, and they do not always terminate charging at the same cell voltage. There is also not complete agreement on how many cells go in a "36V Lithium" battery. It could be 10 Li-Ion at 3.7 V each, or 12 Lithium Iron Phosphate at 3.2 V each, or some other combination.
In theory the BMS should deal with it, but I would prefer to know the specs for the battery and the charger before connecting them. I think both the old and new eZee batteries are 10 cell Li-Ion, but I could be wrong.
Nick