You can reply at any time without jeopardizing your current status. It's only after going through the portal process to land that it gets tricky. Until you land (get your eCOPR), your work permit and TRV are still valid. But once you get your eCOPR, both your work permit and TRV are invalidated and the only way you can return is over the US-Canada land border or with a PR travel document ($50).
Why not tell them in the reply that you are returning after 3 weeks? It's one of the things they ask you for. Then when you come back you write the email address and tell them you've returned. That's what I did. I was in Canada when I got the email but I was leaving a few days later so when I told them this, they put the process on hold until I came back, emailed them, and the process started again the next day, and I was landed a few days later.
The point is, reply.