Example: If i take all the soul gems, will they respawn?

So far, no.
This was a sticking point for many with Hearthfire.
It seems the devs have treated Severin Manor like the city houses we love to decorate....so far.

Edit: A cheap test would be to take the cabbages off the kitchen's barrel. Leave the manor for 31 days then see if they've returned.
Whether they return or not will give you the answer.
Hope that helps

Nothing respawns, the house clean up code will return those two skulls to the display case though. I have not got the plants to grow back either but was only waiting 10 days, maybe they need 30? The plants and contents if the urns outside in Raven Rock only take 10 days to respawn so I just decided not picking the inside plants was best, we have plenty to pick outside.

Unfortunately my game does not run the best in the house, so while I have collected most of my house decorating supplies, I have not really done anything yet. I will probably wait for the next patch to see if Bethesda can get the game to run a bit better. I usually only go in for house decorating when I am tired of doing quests, or someone gives me a house to build as a quest. So it might take me a while to decorate Severin Manor.