The charger will likely show less mAh after charging them because their capacity rating, which if they're still new batteries is 3000mAh, will have gone down so if you are making sure you discharge to half the capacity before recharging, then yes, usually. But I should add that if the charger features a protection timer the goal of which is to make it stop charging in the possible event that the severely aged battery is taking much too long to be charged, then if that's what caused it to stop charging, the mAh shown by the charger might not be accurate. Usually a reduced capacity is the first sign of battery aging, as it happens normally, always. (Even, if the battery isn't getting used.) It is a normal part of how the battery chemistry in a lithium ion rechargeable battery works. The mAh number shown by the charger is usually, but not always, a useful indicator of the amount of aging that has occurred. There could be other factors that throw off this number because different chargers react differently to what they monitor, how they monitor, and how they react to what they monitor. There could be properties at work like temperature, or if the battery doesn't hold its charge too well in a severely aged battery the internal resistance, or possible damage it took due to weak spots in the manufacturing process if they went undetected during the manufacturing process so damage causing all sorts of issues or off-behavior in the battery leading to what the charger expects from the battery. Therefore the answer to your question is we don't know.
