First, prune the savefile so that only the chunks that you want are saved.
Then you need to delete the following files within the "ftblauncher\BlastOff\minecraft\saves\(yoursavefile)\" directory:
(example: within the "ftblauncher\BlastOff\minecraft\saves\EzCore1.2.8" directory)
Code:
RuinsPositionsFile.txt
AE2\compass (the entire directory)
AE2\spawndata (the entire directory)
data\EnviroCaveData
data\EnviroEarthquakes
data\EnviroMineshafts
data\metCrashedChunks.dat
data\metGhostMets.dat
data\ruinschunklogger.dat
data\Stronghold.dat
data\villages.dat
weather2\VolcanoData.dat (and all of the backup files for VolcanoData.dat)
And if you really want to make sure that you get random terrain generation, repeat all of the above for the savefile within the "ftblauncher\BlastOff\minecraft\template" directory. (Pruning of the map and deleting of the files and directories listed above.)