I've found these three important manuscript components, once broken, can never be fully restored. But I'm a gardener, and I always try to fix broken. I know three ways, in fact.
If a plant takes a long time to grow from seed, graft a branch onto more established, ordinary rootstock. Lots of fruit growers use this method, and every Japanese maple I own is a graft.
Applied to writing, a graft might be a chapter which didn't work in one place, repositioned in another. I find this a messy solution. There's usually a big ole knot where the graft is, and it can't be smoothed out. Plus, if my chapter can move, it must not be a strong part of the story arc. Best to cut it and move on, I say. A graft CAN work for a smaller section like a particular bit of exposition.
If a plant is withering or blighted, cut the whole thing back to the root. Severe, but sometimes necessary. New growth is always stronger, and the established root means it will fill out quicker. Note: Works best on perennials and some shrubs.
In my writing, I only have the heart to apply this method to an early draft of a manuscript. I'll go back to the query, adjust, and then draft again.
Horticulturists use this method to make more of something they value, without diluting the genes through pollination. A tag reading "asexual reproduction prohibited" probably means the plant you're buying was grown from a cutting. Things like boxwood and hydrangeas do well with this method. I also use this method when voles get at the roots of something I love.
An example of cuttings used in writing: companion novels. Take a character from one story, plant her on a blank page, and spin a whole new story. I haven't had the chance to try this yet, but I've got an idea floating around for a secondary character, involving Hittite castles and terror birds. It works in my head anyway.
The literary equivalent of a vole?