Can delete some blocks with lump files.
There was an altered version of sacrifice part 3 in that thread below but unfortunately it got deleted.
That download included a vpk including nav file and lmp file.
It was completely serverside, you only had to place the vpk on the servers addon folder.
In that map the fence was opened in the last map, so you could climb over the blocked fence to reach the back parts of that map.
According to dragokas you can put lmp file directly on the server map folder too...
See short discussion part here.
Never tried that myself yet but you may pm dragokas if he is still around.
Then you only need to make custom nav for that altered map.
Good video is here about how to create custom nav.
Make backups of your map folder first...
Personally I open the game in single player, then sv_cheats 1
Then load the map you want to edit.
Then do whatever you want to edit there.
Then always do the nav analyse
When everything works you can upload the nav file you just saved to the servers nav folder, that would be serverside then.
Restore your local map folder and then you see when you connect to your server, it is still custom nav.
That way you can block a path with stripper and make the nav around that block so bots won't get stuck etc. It is really fun to play around with that.