Because of the many changes to the mods in the new packs it is recommended to restart the server completely. If you really want to try to update your server to the mindcrack pack try replacing the mods, miscperipherals, lib, and the coremods folders. You obviously have to replace the old jar with the mindcrack.jar. I haven't done this with my FTB server since I just restarted it but those are the things I would try in order to make it work. Keep in mind that the mindcrack modpack is different than the beta pack so thing will probably be missing if you do get it to work.
