@Ray ********
unless I'm mistaken you ONLY get that letter (asking the stamps be transferred to the new passport) when you get your new passport INSIDE thailand. They don't give you that letter when you get your passport renewed in your country.
you won't have ANY issues showing up to thailand and handing the officer at passport control your old (cancelled) passport that has your still valid extension and re-entry permit in it AND your new passport.
They'll stamp you in on the new passport
Then before your next 90 day report, you can go to your immigration office where you got the extension to get the stamps transferred to the new passport