Do I need to check back in with local immigration upon returning to Thailand if I have a re-entry permit and my 90-day report is still valid?

As Tod said and keep current with the rule. My Province of Chumphon never required the TM30 the first 3 years or so I was here. Then bang, without notice they started requiring it. You just never know what’s current or not.

Which 90 days? Your 90 days Non O visa? Just saying 90 days is not clear. Could be many things.

I believe you are mixing up two separate things

For a 90 day report, when you leave the country before it's due, the 90 days starts counting down again when you return and your NEXT 90 day report is due 89 days from the date you stamp back into the country. The day you stamp in is day one..

And as far as you 'checking back in', that's a TM30 <- notification of foreigner in residence form. SOME offices say if you're coming back to your primary address you don't need to re-file, BUT with that being said, SOME offices say you do. So check with your office once you're back and see if you have to file a new TM30