Which resources/files did you remove in SimPE? Just the PropertySets?
If you use the age ticks in the hair binner, it removes the proper ages for you, and does so properly. You shouldn't remove any other resource files in SimPE after that. Hair files are a bit (in lack of a better word) moody, so if you remove the wrong resources, they can sometimes do unexpected things. You can remove PropertySet files, but let the Hair Binner take care of the rest (and don't delete 3DIRs, this can cause a huge mess).
The "HairXML" sees the base hairs as black and brown (because the bases were black and brown), but they are properly binned as grey and should show in the elder/grey bin. The grey hairs binned as blonde and red will be recognized as red and blonde even in the grey bin. Like I said, that elder/grey hair bin is strange.
It gets weirder with the hairs that only has one grey per family, though (I think those default to the color they're originally linked to, without saying it for sure), and greys that don't have younger ages and aren't family-linked will randomize to just about any hair if the sim is de-aged to adult.