Setting back the anchored category can solve your issue, anyway digging further
1) You should never modify the core file, insead look into the file in
If you are referring to the Layred Navigation with subcategories look here
2) also look for the page layout for the category in custom design settings. If it is one column that will also show blank if you do not have any product allotted to parent category but to only sub categories.
If you have alloted products to subcategories only, and not the parent category (which is obvious) , and parent category is not anchored then it does not show the Products either from its subcategories too.