A year of half-assed online work could have a pretty big impact. Many schools weren’t well prepared to run classes online.
I also saw a separate Japanese study that showed more lasting effects in lower income families, with scores mostly bouncing back in others. But that’s Japan, hard to generalize with how they do schooling and out-of-school study.
One possible alternative explanation is that all the kids were stressed out of their minds because there was a killer virus on the loose and no one could focus in school or outside. If you want to guess at gender differences, one might be that girls care about other people more, and so were more stressed out by the thought of their parents or grandparents dying. I don't really think girls care that much more than boys though. There would need to be some kind of retrospective ethnographic study to figure out what the heck happened.
Another explanation could be that since the kids were used to distribute viruses to reopen the economy, their health suffered. There is ample documentation that women get long covid more frequently than men.
From speaking to parents during this time, many were unhappy with the rigor of remote work and the quality of instruction during this period.