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I recently noticed that some of my Lupins after i pruned them just had a little stump left which has gone brown. I dug them up and they didn't have a lot of roots, think they might have been rotting so i put them in a pot and put them in my greenhouse for the winter. Will they grow back and if so do i need to water them in these pots over the winter? All that is there at the moment is a sorry looking brown stump
You should let lupins die down naturally - they certainly don't need pruning.
Providing the roots didn't get too damaged by the wet, they should produce new shoots in spring. Keep them moist in your greenhouse over winter - just damp, not soggy.
The title of your post is 'potted lupins'.
As you must know, lupins are especially susceptible to damage by slugs. I've never grown lupins in pots myself, but that may help to reduce slug damage a little bit. Come Spring, they may have a better chance of growing in a pot, than in open ground.