If you want to support both brands in the future, create a SchLib symbol for each, place them on the schematic and connect them in parallel. Create two Assembly Variants, one with all "LED A" and the other with "LED B". Update the PCB and place all the new "LED B" footprints over the "LED A" ones. (Since AD15, this can also be done within a single symbol, by specifying a variant component from the library; multiple parts don't need to clutter up the schematic then.)
The result is that Pick-And-Place information will be outputted with the correct rotation for either variant.
If you don't need a compatible solution and just want to update them all, then go to Tools/Footprint Manager and edit the footprints for the correct pinout; update PCB, select all the LEDs and, in the Inspector, set Rotation to "Rotation+180".
Or just add a note to the assembler that the different LED parts are wired backwards. They may even figure it out on their own, because footprints have inconsistent position and angle references.
Tim