I think I can answer some of your questions.
I wanted him to use the Thai passport for the trip to Thailand soon and not his NZ one. The idea was that he would show his NZ passport when we are coming back to the airline but it would have no departure stamp on it from NZ.
So three different things: the airline, Thai immigration and NZ immigration.
You can show the airline both passports (they might ask this when departing from Thailand when they see no entry stamps in their NZ passport; they will also want to see the NZ passport because there is no NZ visa in the Thai passport), the Thai passport will show them that your partner (the one having both passports) will have no problems clearing Thai immigration (both ways, going in and out of Thailand, because they are a citizen). The NZ passport will show the same for their entry / leaving NZ.
When passing Thai immigration your partner can choose to go with their Thai passport (in my experience this is the easiest, also when staying longer they won't need a visa), just make sure it's the same (or a new Thai passport) on the way in as it is on their way out. Thai citizens (using their Thai passports) may pass the border using an automated machine (assuming their passport has biometrics, they probably do, you can check if it has the biometric sign; also assuming they leave via an airport with those machines, land borders don't have them, as far as I know).
If they have a NZ passport they could also use that (in Thailand), but there isn't really any point (as far as I can see) to doing so.
If your partner joins the queue for foreigners, their NZ passport will be checked by a Thai immigration official (just like any other NZ citizen). If they entered using their Thai passport and they leave using their NZ passport, they will have a problem because of the lack of stamps (it will look as if they entered the country illegally), so don't do that.
Just like you, they will have to identify using their NZ passport to gain entry to (and leave) NZ.
Or as it is electronic, are the passports only scanned for Thais at point of entry by a machine , like here for NZ Citizens and what would be the likely problems on departure.
This depends, if you go through the machine, it's not checked by an immigration official. If the machines are out of order (could be?), you end up in a queue with an official rather than a machine or there are no machines at your point of entry / exit then you will face an immigration official.
He has property now in Thailand which I do not want to Jeopardise. Would it be a problem for him to travel on his NZ passport.
To the best of my knowledge, his property has nothing to with his passport (many Thais don't have passports but they do identify using a national ID card). It is probably under the administration of the Department of Lands, to which your partner will identify using their Thai identity card (as opposed to their passport). If they do not have a (valid) ID card they should get one at the municipality office where they are registered.
Having that ID card is very important, this is what they would use if they are stopped by police or have to identify themselves anywhere else in Thailand (after passing the border). As a rule of thumb, when you need to show your passport to show that you are in the country legally, they show their ID card (much like you probably don't always carry around your passport in your own country of NZ).
No stamps in the Thai passports
I also see you're concerned about the lack of stamps in the Thai passports when entering Thailand. This really isn't a problem. Inconsistencies in the stamps by Thai immigration are common, because you will not get stamps when entering or exiting through a machine.
Lack of stamps from other countries are also common since many Thais travel abroad using a second (foreign) passport.