I always do it with my tomatoes, partly because i always let them get too leggy before i pot them on, and also because i pot them from 3/4 in pots into their final positions in 12 inch whoppas. I've not found it reduces the crop at all - in fact i always have far too many tomatoes!
What I am saying is that it is not ideal to grow leggy plants and repot them at a deeper level, notwithstanding the fact that it is sometimes necessary because we are too eager to get going
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