If the tomato plants are diseased, the bagged flowers might abort.
I tried bagging the first pepper blossoms this past summer and many did fall off. I don't know how much the bag contributed. Then I started putting the bag over the whole stem, trying to avoid any bag/flower contact. The less it touched the flower, the better it worked. Maybe later flowers are tougher or maybe all pepper flowers hate to be touched; I don't know.
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