I have a problem with overlay mode for objects in Inkscape, i don't get the result that i want!
here's an image in Inkscape :
And here's an image of what i want using Synfig :
So why it's not working the same

Thank you.
It doesn't look like that part of the circle did disappear in Synfig, or else we would not see the stroke still remaining
If you can tell us what you want to do, we can tell you how.
If all you want is for that outer part of the dark green circle to disappear, then do this:
1 -- duplicate the dark green circle
2 -- select the light green circle and 1 dark green circle
3 -- Path menu > Intersection
Do you have some transparency in the other object (the light green one) or maybe alpha transparency in the dark green one? The only way I can get result like yours is to make one of the circles partially transparent. Or do you maybe have some filter applied to the other objects or layer?
To make it work, add a new layer and set its blending mode to anything custom.
Then you can turn that layer off, the "per object" overlay filter should work as expected.
Does synfig support clips?