Hello newby here
Having problems with a 40va transformer burning out on an AC unit I'm currently working on. It is an older unit with a fan center/motor control board? (a transformer with a low voltage junction block on top of it and a fan relay mounted next to it.) Complaint was indoor fan not working found had no 24V from xrsfrmr and the back of it looked burned. Replaced the fan center board and new xrsfrmr burned out once again on primary side (OL) on ohm meter. Motor tested fine ran well. My question is since this is obviously a short somewhere should I be concentrating on the primary side circuits or can a low voltage short burn out the primary side? Supply voltage to unit tested OK. Any help appreciated.

Start checking the low voltage circuits for a short or overload condition. Use a small inline fuse holder from radio shack or others to protest the transformer while testing OR get a small resetable circuit breaker device like I have and that way you will not have to keep buying fuses while you are testing.

Look for pinched/cut wires. Many times they can be in a wall going to the thermostat. Try labeling then disconnecting the thermostat at the furnace/air handler to start with since the thermostat wirng seems to be where many of these kind of problems originate. Happy Hunting.

Thank you, I will start there.

A 3 Amp automotive fuseholder on the secondary works.

I have a post somewhere where I suggest 2 particular automotive lamps in series as the "fuse". When you find the short, the light comes on. Select 12 lamps that draw no more that 40 watts and pu them in series.