What I do is delete the unused chunks and move the world over anyway. Yes you will lose some stuff but most of it will be fine depending on what the mods changed.
I delete the unused chunks because with power armor you can explore a lot of the map with flying, witch makes the world files really large.
I am in the same boat you are, I had a MC sever as soon as multiplayer was released. I just updated it over the updates and the group was happy. We started playing Tekkit before tekkit 3 ( i forget what it was called back then ) It was fun in all but after many new worlds the group started to get annoyed, and so did I.
If you delete unused chunk retogen works pretty well, you still have to rebuild some stuff in the updates but it works pretty well. Tell your members to put some stuff ( To help get power back on )in vanilla chest as your AE system will most likely have no power. It is possible