My concern here is not so much the IAS/TAS split - yes you are actually going faster at the higher TAS but the dynamic pressure and therefore the force on the flaps varies with the IAS. Not sure why some aircraft have an altitude limit but it may be a function of mach number (wild speculation).
My concern is about fatigue on the flaps and in particular the mounting structure. The flaps were probably not designed to be extended at close to their limiting speed from cruise altitude down to landing and this practice may well have a fatigue impact over time. Key point is to make sure that the engineers understand how the aircraft is being used and determine what might require additional or more frequent inspection.