Okay, I don't know exactly what you are doing, and I don't know why it is not working. However, as messing with the data files is a pain in the ass, and can cause things to break, and should not be done lightly, I am going to give this one more go, and this is the last attempt that I am going to make---if it doesn't work, you are just going to have to live with the bug (either finish the level in one go, or accept that there will be triffids).
- Unarchive main.dat which is a .rar archive. When you unarchive it, a new subdirectory called "data/" should be created in the same directory as main.dat.
- In general, anything in data/ will override anything in main.dat. So, if you make a change to files in data/, those changes should be reflected in the game. Hence, do not rearchive the directory, and do not overwrite the original main.dat with anything. If you have already done so, it might be wise to reinstall Darwinia.
- In data/levels/, find the map file which corresponds to the level that you are playing. It should be called something like "map_[levelname].txt". Open that file in a text editor, and delete any lines in the Buildings_Definitions section of the file that begin "Triffid." This will remove any triffids that are being loaded from the map file. If there are no triffids in the map file, then you are done. Save any changes; do not rearchive the directory.
- Next, find your user profile. There will be a directory called "users/"---the exact location varies with OS and the version of the game (i.e. Steam vs retail). There should be a subdirectory for the profile that you are using (i.e. users/[profilename]/). Open that subdirectory. This directory should contain a file called game.txt, as well as several mission files, all of which are encrypted (by the way, encrypted is spelt with a "y") using redshirt2.
- Find the mission file that corresponds to the level that you are having trouble with. It should be named something like "mission_[levelname]_[foo].txt." Use whatever utility that you are using to decrypt the file. At this point, you can replace the original, encrypted version of the file with the new, unencrypted version.
- Open the newly unencrypted file, and, as with the map file, delete any lines in the buildings section that refer to triffids. Save the file. Do not re-encrypt it. The game can understand plain text files just fine.
- Open Darwinia, and load the level that you are editing. If you have done everything as instructed, the level should now be free of triffids. If not, check to make sure that you are using the right profile (i.e. you are using the profile that corresponds to the files you edited).
As I originally stated, after NeatNit suggested that you just ignore the problem, you have two options: the first is to ignore the problem---you can beat the game without destroying every enemy unit; the second is the edit the files, which is not guaranteed to work, is not the easiest thing in the world to do, and can break things. At this point, I have given you all of the tools that I know how to give you, so if you are still having problems, I can't help you. Sorry.