I have a trane AC/heat pump unit, and a Trand XE80 furnace.

* The AC is running and all of the sudden it sounds like distant thunder where the heater is at? A fan issue?

Possibly fan. I would take covers off and get a closer look to find where the noise is originating from.

Does it still do the thunder?
All the time or at start up or shut down only

Like dad77 said pull the cover and do a visiual look see
If it does it all the time ,feel inside the inside if blower cage, maybe a piece of paper or dead varmit throwing the blower cage out of balance

Change your filter... if your filter is dirty the unit will try to pull air from anywahere and can cause thunderlike sounds at startup an dshutdown.

My parents had the same issue last year, they had to have a part replaced. To be on the safe side I would contact a repairman to come out and have a look