When a character ages, there are negative penalties to physical stats.
As a made up example, if there was a commoner who somehow had 3 in one or more of their physical stats at age 18, and due to a very unlikely fortunate event found a manual corresponding to their weak stat, granting them a +3... what will happen to that stat once they reach old age?
I am assuming that equipment, psionic, and magic based bonuses are not affected by aging.
The ability has a base score of 3, a +3 inherent bonus from the manual, already has a −1 penalty from middle age, and reaches old age for a further, cumulative, −2 penalty. They therefore have a score of 3 + 3 − 1 − 2 = 3, which means they have a −4 modifier.
No bonuses, or penalties, or any other modifiers, are affected by aging. That is, you do not add or subtract anything from any of your other bonuses or penalties due to aging—you add or subtract your aging modifiers from the score, just as you add other bonuses or subtract other penalties from that score. Aging is just another modifier to the score, and so is applied to the score alongside any other modifiers. All of the modifiers are applied in full (barring special cases, which none of these are).
The stat will be back down to 3 at old age.
Bonuses and penalties in 3.5e don’t really ‘interact’ or modify each other except for one specific rule that I will cover in a moment. So computing a given score consists of simply taking the base score, adding any bonuses to it, then subtracting any penalties. Some of the penalties may cancel out some of the bonuses (or even completely negate all of the bonuses), but those bonuses do still exist. They don’t just disappear because of the penalties.
The ordering in this case is also important, because aging (and a number of other sources of penalties) cannot reduce a score below 1 (so if you applied the penalty first, the total would be 4 instead of 3). That order is intentional so that penalties, which are often less common than bonuses, apply to the fullest extent possible no matter what the score.
The one special exception to all of this is if you have bonuses or penalties of the same type applied to the same score. As an example, say you have a Belt of Giant Strength +6, granting you a +6 enhancement bonus to your strength score, and then somebody casts Bull’s Strength on you, which grants a +4 enhancement bonus to your strength score. Because both provide an enhancement bonus, you would only have a total of +6 to your strength score because that’s the higher bonus. This is usually most relevant with armor, shield, enhancement, and morale bonuses (those four are the big ones that have lots of things that grant them), but it crops up with other types as well from time to time.
However, that exception does not apply in this case, because aging penalties and bonuses are untyped (or, alternatively, they have a type of ‘aging’, and are the only instance of that type of bonus or penalty in the game, meaning they are effectively untyped), which means they are only cancelled out by effects that specifically call them out as not applying (such as the Monk’s level 17 class ability Timeless Body, which explicitly states that the monk is no longer affected by penalties to ability scores from aging). This is distinctly different from an inherent bonus (or penalty) such as provided by the tomes or manuals, the term ‘inherent’ is just a (rare) type of bonus, it means nothing special beyond identifying the type of bonus.
