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Well,the biggest concern when repotting autoflowers is shocking the roots,which consequently stunts the plant's growth for up to 7 days or more which is significant, because most autoflowers live only between 60-90 days,and as you wrote bottom ones came off or are damaged is not good at all ,autoflowers should be planted in final pot from seed ,even if she survive and will continue to grow again your harvest might be decreases.

Transplanting autoflower plants is not recommended and you need to be very gentle with it to avoid damage the roots. when the roots get damaged the plant will go into shock. shock can be stunted growth and lower yields. The plant will be trying to recover from the damaged roots. This can also force it to flower earlier then normal. Do everything in your power to avoid damaging the roots, using microbe inoculants and if possible don't transplant. I would still grow out your plant, but be wise as it will not be eating as much in recovery and if its really stressed out it will hermi on you. So watch out for balls and nanners. Best of luck