Messy photo library

i had trouble with my external drive with all my photos on. sadly my back up was not working as it should, either. but i have a techy friend who moved the folders over to a new external drive. but i doing in so it became necessary to move the same folders more than once. i now have som duplicate folders (even if they have different sizes). when i have cleaned up the mess, will C1 be able to relocate the photos, they might not be in the same kind of folder system? or should i just build a new catalog? will all organizising in C1 disappear then?