I don't have the time to dive deep into this article, but I would not be surprised if there were wasn't enough evidence at 12 months. It's a process which takes years, as with puberty itself.

The TLDR is that there are several issues with the study methods which are apparent from available materials (and probably even more apparent from the actual study data which has been withheld by the authors). The cohort that received gender affirming care over the twelve months showed no improvement over baseline, while the control cohort deteriorated into even higher levels of depression/anxiety/suicidality. Instead of looking at the treatment group and saying "there has been no improvement", they compared it to the control and said "they haven't deteriorated like these people have."

Unfortunately, the vast majority of the control cohort simply stopped responding to the survey over 12 months, so there is no end to potential confounding factors causing children (who for all we know elected not to receive gender affirming care to begin with) to stop responding to a survey issued by a gender clinic, or the confounding factors that caused the others not receiving treatment to remain in the study.

I've seen this argument many times and these same sets of studies referenced, yet never is it mentioned that the recorded results are absolutely not single variable measurable items. There are nearly infinite alternative explanations for both sides of the argument, if you are clever enough to break free of the desired outcome bias.

The article touches a little bit about how responses to a 0-27 point depression questionnaire are coded as 0 or 1, 1 being "has moderate to severe depression" and 0 being "does not have moderate to severe depression" at a threshold of 10 points or higher. Similar situation for suicidality. Instead of tracking the actual point changes across the 12 months, they just tracked the pooled percentages of 0 vs. 1.