(Eggplants & tomatoes belong to the same family and these answers apply to both.)
1) Were both beds of plants healthy? Were they the same variety, and do they look and grow the same? The bed that failed to produce fruit – were the plants continuing to be healthy, or did they stop growing and show signs of disease, etc.? Only if they were sick is there a problem with the soil, in which case you may need to treat or sterilize the soil.
To sterilize the soil, the best thing is methyl bromide, which takes 24 hours and kills everything, so use extreme caution! However, to use it in a greenhouse you must have a full body suit with outside supplied air. It can be fatal in even small doses in enclosed areas. Otherwise you could use steam, if you can get enough to hold the temperature at 200 degrees F for 2 hours. Either way, you must cover the bed tightly with plastic.
If the two beds of eggplant looked the same you do not need to sterilize the soil. Methyl Bromide is a chemical that is very effective at killing everything – but it is getting harder to find, and very expensive. And in the USA it requires a Pesticide Applicator’s license to even buy or use it. Steam equipment is also expensive, and unless you have a steam-heat source that you could tap into, it probably isn’t practical either. With the extremely cold winters you have (-30 C), many bugs and disease pathogens are killed, so I will be surprised if your problem is a disease in the soil.
2) If the plants were healthy, but just did not produce fruit, then the problem is most likely in the pollination somewhere. Eggplants are self-pollinating, so you do not need to help them, and you could have actually caused the problem – if the brush was too wet, or if it was diseased or something. If it was too wet – either the brush or the environment – that could inhibit the transfer of pollen also. Were you using the same brush to pollinate both rows? And were you pollinating both rows the same day? If so, then it isn’t the brush, but some environmental difference. Try just shaking or vibrating the plants to make the pollen transfer if there is no air movement in your greenhouse.
3) What about the light factor? Did both beds get the same amount of sunlight? Fruiting plants must have uniform, sustained light all day – otherwise they produce greenery, but no fruit.
4) Eggplants like warm temperatures also, in addition to lots of light. Was one bed subject to more cold air than the other – such as being planted closer to the greenhouse wall? If the temperature goes below 60 degrees, sometimes frost-sensitive and frost-intolerant plants won’t produce fruit. Was there any difference in temperature at critical times between the two beds?
5) Also, some insects will eat the pollen, such as ants. Is that a possibility? However it would be unusual to have insects attack one bed and not the adjacent one.
6) Were the two beds planted at the same time, so that the plants were the same size? If not, conditions might have been different when the second one was flowering (although the flowering continues for months – so that isn’t likely), or the taller row was shading the shorter row.
7) What time of day did you pollinate? If it is done before the male flower is fully open, the pollen is green and won’t fertilize. Also, after the female flower starts to collapse it is too old, and won’t accept pollination.
8) Is there a possibility your one box had nematodes in the roots? If the plants are carrying nematodes, they may look healthy, but they can’t support the nematodes and bear fruit at the same time, and since they can’t get rid of the nematodes, they abort the fruit and just keep on trying, without success.
9) If you pollinate using a male from the same plant, you have more risk of not getting good fruit – it’s better to use a male from a different plant and cross-pollinate.
You really have to become a detective to discover what happened, don’t you! Let me know the answers to the above, and maybe we can narrow it down and find the most likely cause of the problem.