Will I face issues transferring my immigration stamps since I did not receive an exit stamp when leaving Thailand?

Cannot you not renew passport in country.

Just a note, make sure you use the NEW passport number when you file the TDAC (Thailand Digital Arrival Card) coming back into the country :)

No

You went thru the auto-departure gates (automatic out) without getting a hard exit stamp but you were still stamped out of thailand in the system

When you return you present BOTH passports to stamp in. They will stamp you in on the new passport and make a notation that your extension/re-entry is in the old one

Then you take both passports to the immigration office where you got your extension to get the stamps transferred

You will have no problem at all stamping back in to thailand with both passports or with moving the stamps once you're back and go to your immigration office