From experience I think hot peppers need to be pruned or topped once if you like from 30-50 days the growing tip will be pinched out and it will bring out more extra branches,this is usually enough,,even this will push back the maturity period by 2-3 weeks,if you continue to prune it like tomatoes you might end up with a crop that will take 200 days to mature,hot peppers are hardy and tougher than tomatoes by far and naturally when the crop starts out the Y branches in 60-70 days it will start flowering,this is when to switch foliar application to flower and friut booster with higher P and K than N,but to me the single most important step in pepper farm is the variety,if it is not resistant to viral diseases it is a waste of time

I saw this solution: your crops are super and it will be a sacrilege to leave such healthy and good crops to fate,it is not yet late to properly intervene,what I will advice is this,if you still have empty land clear out a portion that you feel will contain at least 30-40 percent of the habanero in the greenhouse,after clearing,dig holes that will be the width and bredth of a shovel blade and one foot deep at straight lines,give it 3 ft spacing in between holes,also each line will be spaced by 3-4 ft from the next you can use nylon twine to make it straight, apply manure inside each hole and turn with shovel.,the holes will serve to conserve water during the dry season,a good containment for manure, fertilizer and manual irrigated water and save stress of ridge making.
Next go inside the habanero green house after serious irrigation , use shovel to remove every next crop,,this will be done in the evening when the sun is down,they will first use the shovel and punch the four corners of the crop and dig in deep from one side,all the root mass will come up in a nice square shape intact,they will carry it outside with the shovel and placed inside the hole and watered,next morning it will be irrigated before sun comes,nothing will happen, to it,we even retransplant fruiting pepper crop,if you leave that habanero farm like that I am seeing it might be a serious problem that is easily still aviodable,and pls don't even think about pruning as an alternative it will make the crops triple or quadruple in size and grow so many extra stems and foliage that you might mistake your greenhouse farm to be the congo rain forest in a few months time