Can I do my 90-day report online again after re-entering Thailand early?

It doesen't reset, it stays at the origal 90 days. I got fined making this mistake

I had the same situation, and did mine early online. I subsequently did my annual extension at Immigration, and they were happy enough.

You're still required to go to your provincial immigration and check-in after having entered the country.

No, you don't have to, nor should you try, to do it online, in response to the friendly reminder.

After your return to Thailand the new due date for your next 90-day report is 89 days (cuz the entry date is considered 'day 1') after the date of return.

You can try submitting online, if you like, two weeks before the due date, and see what happens. There's an, oh, about 95 percent chance you'd get a REJECTED result, with a directive to report in person to do the report at your local immigration office. It's a given now that the first 90-dayer after returning to Thailand from a trip abroad has to be done in-person. But a small number of folks have gotten an APPROVED on that first submission after returning to the country, so there's no harm in giving it a try.

That’s automated but you’ll need to do it in person as you left

The systems aren't 'connected' the email you got is just an 'automated' thing..

I'm pretty sure you can't do your first one online when you return from abroad... So it is a trip to immigration I'm afraid.

For the sake of uncertainty, visiting immigration isn't too much of a pain, Pop in, They can be great, and hey it can't hurt none.

You should just ignore the automatic email. The system isn't aware you left the country. Your next report will be due 90 days from your arrival, with arrival being day 1, and you'll need to report in person.