chunks resetting in some locations ???

ok so recently there has a been a strip of land over our worlf where the land has decided to regenerate into flatland, at first i was like ugh i have to terraform that now. i have recently started doing so but for some reasonm every time i do anything within these junks and move away and go back into the chunks, everything i just done disappears, it seems to keep resetting those chunks -.- i have run minecraft region fixer which fixed over 200 chunks so i assumed that was solved... nope, still the same issue, i have these huge holes in that land that will forever be there and i dont understand why its doing it!
has anyone else had this issue? or knows ho to fix it?

edit: it turns out if the save-all comamnd is used (my server does this command every 5 minutes) whilst the chunks that i edited are unloaded causes the reset...?????? whyyyyy?

you can see the affected chunks across the world just above spawn, the big holes:
http://mc.xemcorp.com/map/xemcorp/

heres some screenshots:



after i move away and type /save-all



im still in need of help here =S

EDIT by Moderator: merged posts, please use the edit button instead of double posting.

 

update: i have gone over these chunks in mcedit and deleted then placed land within these chunks, loading the server back up and going back to them makes no difference, i dont understand what is causing these chunks to regenerate to flatland.... these chunks are right in the path of a build and without the ability to edit them, the project is not going to continue! regenerating the entire map is not an option due to the fact the world is covered in many peoples builds due to the world being the main world. the world is an ongoing project to create a coherent lore based world.

any help is greatly appreciated!