This is pretty simple :

I'm editing an esp file but after ANY change I do and save even the empty race (race -> ppm - > new and it's completely empty) some "stuff" disappears and this stuff is more precisely the magic effects of some spells so they're invisible in game after. I was editing a script of some spell but to get it work I had to use CK and find it's magic effect of this spell. I did open it and in the right lower corner there's a small window called "papyrus script" and there's script itself. I went to it's properties and had to "auto-fill" some empty values in order to get this script and spell working.

So ... the problem is I can't use CK because of this disappearing magic effects but without CK there's no way to fix these empty values and get script working.

I need to fix these 4 lines somehow manually or make CK stop deleting my stuff. I have some screens of this script and it's view from CK but sadly I can't post links/pics yet ...

The CK doesn't delete stuff. Are you making the plug in that you're loading active? If not any changes you make don't save. Tick the box your the esp and select Make Active, then load.