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Yes that's what that yellowish line is. I don't know if I would say get rid of them but, It should help a little or deter them some. Though it likely wouldn't do a damn thing for the larval stage since its in the plant. But, might help with the adults some.

leaf miner

Top is thrip. That is not what ate the leaves though. You got a couple different things going on here.

If you disturb or lose some roots my guess is yes you will see some transplant shock. I litterly just did something similar in veg due to a change in plans. Went from soil to hempy buckets and they hardened up and didn't grow a lick for two weeks. Starting to pop now. 2 week setback basically.