Gut sounds become reduced during a ride, in large part, because of dehydration, redistribution of body fluids and alterations in body electrolyte concentrations
This has been pretty much my understanding too. Blood is redistributed to working muscles away from the gastrointestinal system. There are changes in the autonomic (ie automatic) nervous system away from the parasympathetic (which services "guts and glands") to the sympathetic (which is all about "fight and flight", exercise etc) which plays a part in changing the blood supply to where it is needed, and also stops the guts from churning away quite so much.
If we keep the horse eating and drinking, various reflexes keep digestion occurring, and there will be further absorption of much needed food and liquid. Not only does the presence of food stimulate the stomach to move, there are also reflexes which tell the next bit of gut to move along to be ready for the food coming through. A perhaps indelicate example of these physiological reflexes is the gastrocolic reflex, where the presence of food in the stomach causes a reflex movement in the large bowel, leading to defaecation (eg usually about 15 minutes after eating breakfast!). So I guess that can explain why although no food has got to the intestines after a feed at a check point, there may be increased noises. Certainly the biggest single factor in maintaining gut noises seems to me to be adequate hydration, and if a horse presents at a check with reduced gut sounds, I use it as an indication to discuss with the rider whether the horse is drinking etc, and how we should best manage the horse.
As someone else mentioned, many horses have quieter gut sounds at the first check - maybe as much to do with sympathetic nervous discharge ("I`m still really excited about going on this ride today and seeing all my friends!") as how much they have sweated and drunk.
What about probiotics and the like? I know of people who have great success with them and some who don`t. I don`t know that giving probiotics during a ride will help, but giving them for a few days before seems to be useful for some. Perhaps it improves overall digestion and the horses start off with a better GI status. Feeding after a ride will help repopulate the gut - GI flora can die as a result of decreased throughput, excess heat of the gut, relative dehydration etc, which can all happen during an endurance ride. How many of the bugs actually make it through the acid stomach and down to the intestines is a matter of speculation. However, if it works for your horse, go for it, I say!
The other factor which may help with maintaining normal fluid within the GI system and therefore gut sounds (in the face of all else being normal) is adequate fibre in the diet. I have made this statement deliberately vague, as adequate varies from horse to horse to ride. If in doubt, perhaps consult your local trusted professional.
Happy riding, Anne
Murdoch University, Western Australia