Geo's, are "sand sifters" and in nature live in areas where sand is the dominant substrate.
I have used PFS with Geo's since the 1980s, without a problem.
I cannot give reason why your Geo's die, but I do know sand is not the cause.
I will say 40% water change is a bit wimpy for fish that live in rivers, where the water is totally changed by riverine flow every second, during certain seasons.
Are you quarantining any new fish? for proper duration? or just tossing them in when you buy them?
It could be that at some point, a bacteria was inadvertently introduced that is chronic in nature, and kills over time. And has set up shop in your tanks.
Many Geo's come from waters high in tannins, and those tannins keep certain bacteria in check.
These bacteria may not be "acutely" infectious, but become a chronic nuisance to susceptible species over time.
Some Amazonian and northern S American fish kept in aquariums do not always die but are prone to infections (I've seen many severums with nasty HITH, others such as oscars come to mind), if not kept in tannin infused waters. Geo's may be just more sensitive, and actually succumb.
Also consider season changes Amazon fish have evolved to live in. During rainy season, they may live for months in white water, but during the dry season tannins constantly build up (black water, where pH can drop to almost 4) these seasonal changes may provide a temporary purge or cleansing, reducing bacteria numbers.
Here is a pic I took of the the substrate in the Mendahuaca river in Colombia.
Looks and felt a lot like PFS to me.

I have used PFS with Geo's since the 1980s, without a problem.
I cannot give reason why your Geo's die, but I do know sand is not the cause.
I will say 40% water change is a bit wimpy for fish that live in rivers, where the water is totally changed by riverine flow every second, during certain seasons.
Are you quarantining any new fish? for proper duration? or just tossing them in when you buy them?
It could be that at some point, a bacteria was inadvertently introduced that is chronic in nature, and kills over time. And has set up shop in your tanks.
Many Geo's come from waters high in tannins, and those tannins keep certain bacteria in check.
These bacteria may not be "acutely" infectious, but become a chronic nuisance to susceptible species over time.
Some Amazonian and northern S American fish kept in aquariums do not always die but are prone to infections (I've seen many severums with nasty HITH, others such as oscars come to mind), if not kept in tannin infused waters. Geo's may be just more sensitive, and actually succumb.
Also consider season changes Amazon fish have evolved to live in. During rainy season, they may live for months in white water, but during the dry season tannins constantly build up (black water, where pH can drop to almost 4) these seasonal changes may provide a temporary purge or cleansing, reducing bacteria numbers.
Here is a pic I took of the the substrate in the Mendahuaca river in Colombia.
Looks and felt a lot like PFS to me.
