I would delete the chunks from the region files using MCEdit, and then Minecraft will automatically regenerate them when the chunks are next loaded by someone walking past. There are in game methods such as WorldEdit, but I personally prefer using the offline editor MCEdit for such tasks.
Download MCEdit here
http://www.mcedit.net/.
Create a working directory for MCEdit, I have a folder in MyDocuments. That working directory should contain your level.dat, and also a subdirectory called "region". The region files that you are editing go in there.
You will find your server's region files for the overworld in the folder "DW20world/region". Different dimensions have their region files in different folders. To find which region file/s you need to edit, grab the coordinates of the problem area. You will need to convert these block coordinates into region coordinates. The formula is regionX = (blockX / 512) and same for Z. You must then round the number down to the next whole number. Make sure you understand how to round down negative numbers, they get more negative which can seem a little counter intuitive. (+0.5 rounded down is 0, -0.5 rounded down is -1, -1.25 rounded down is -2, etc).
The region files are named r.<regionX>.<regionZ>.mca where regionX and regionZ are the region coordinates. Download / copy the region files you need and put them into the region folder in your MCEdit working directory.
Keep a backup of the region files you are about to edit!
Open up MCEdit, Click open a level... and then select the level.dat file inside your working directory. When the level is loaded, press ctrl+g and teleport to the area you wish to edit (use the block coordinates from before). Fly up high with Q (Z do descend) and get a birds-eye view of the area. To look down at the ground hold right-click and move mouse around.
On the toolbar at the bottom, click on the far right for chunk controls. Click and drag on the map to select the chunks you wish to delete. After making your selection select "delete" from the menu on the left and confirm. Close MCEdit, you're done.
Stop your server (important), upload the region files back to your server, then start the server again.
Of course I make no guarantees that the terrain gen will be less derpy the second time around!
I realise that this is a lot to learn, but if (when
) you get a block on your map that crashes the server, MCEdit can be very useful for removing that block. Crash reports will often list the coordinates of any problem blocks, if a ticking tile entity is responsible for the crash. The only way to rescue your map in that case is to use MCEdit and surgically remove any blocks causing the crash, or use a previous map backup. MCEdit can also fix any corrupt region files you may have, and is fully compatible with blocks from mods. In short, it's worth getting to know how to use MCEdit.