There have been issues with large ID and ImageJ. The nrrd image is converted to float 32 bits in ImageJ, which leads to a precision loss for large IDs. For instance 606826624 and 606826625 will be both converted to the same 6.068226e8 value, resulting in indistinguishable labels.
I am curious though: why were such big label numbers chosen, given that there are way less than 2e16 labels in the atlas ? Is there a particular meaning to these big numbers ?