It is important to know the material of pipe as already pointed out desalinated water is highly corrosive and if pipe is MS/CS/CI and uncoated, corrosion products could be dissolving in water.
It could be basic however would like to point out (sometimes sampling points's selection plays a vital role);
Please check if your pH meter is calibrated (must be installed at Product of RO or RO Product Tank)
Please check your pH meter is calibrated at Receiving End means if it is coming into a Reservoir (20km Away).
Check your RO Product Tank Reservoir if not having any infiltration of the ground as instantly coming out of your RO pH might be around 6 - 7 and you might be measuring at that point but look into the Product Tank (reservoir from where you are pumping towards 20km).
Check your Receiving End Reservoir (20km Away) if it is not having infiltration or leakages.
Check pH just from the pump discharge from RO Product and pH at the reception tank inlet pipe before entering into the reception tank.
The above checks will ensure if we need to look into the pipe line or not, first ensure these points. I strongly feel your sampling point will play a vital role.
If all are Ok on these, then there must be Pressure Release Valves/Surge Release Valves on elevated points of pipeline due to topography , please check any of these points are intact or are not the reason for any infiltration.
Please check further detailed analysis of water for RO Product, RO Product Reservoir, Before Entering Reception (20km away) and from Reception Reservoir;
pH
TDS
Conductivity
Hardness
Alkalinity (Methyl Orange Alkalinity)
Phenolphthalein Alkalinity
This will help you if other parameters are also not changed.
Hope you will find now the main cause and solve this issue. Please share your findings.
Dissolution of salts deposited in the inner walls of the pipe could be a reason. Measuring EC of water prior to and after passage through pipe network could verify this hypothesis.
Slight acidification of water before transmissipn could be persisted till EC of transmitted water reduces to desired levels.
If the pipe line laid below the ground and pressure and flow of the water transmission line are not stable through out the process , then definitely the your water is continuously contacted with foreign material.
Try chlorine dosing to regulate your pH, it will gives you other benefits too I guess.
Normal chlorine dosing for disinfection purposes has a small effect on pH. If it's gas chlorine will slightly lower, if it's sodium hypochlorite will sligtly increase it. Chlorine is a disinfectant and not a pH-regulator.
We had same experience with cement mortar lined steel pipe. It was temporary and after months lowering the quality of water declined. Finally, the quality stayed stable.
One likely cause is leaching from the inside surface of the pipeline if it is cementitious? If this is the case it is unlikely to change with time to any extent and it could lead to erosion of the pipeline. It may be possible to reduce the buffering capacity of the water or alternatively to consider lining the pipeline with a coating such as an epoxy resin. Or you could draw a polyethylene pipe inside the existing - sliplining. Logistics and size will govern the decision.