It is unrealistic that you will get the exact money back that you put into your car. If you spend $ 10,000 worth of mods, depending on what they are, you could get a percentage back from them. That is, if you decide to keep them. For example, if you spend $ 5,000 in a set of wheels, but keep your stock ones, you could sell the aftermarket ones when it comes time and get $ 3,000 for them...so technically, would you would only lose some money.
I don't think you would lose ANY money over the value of stock, unless the modifications that you have are not working well w/the car - say for example the tune is off and has hic-cups and hesitation or it is running rough, etc. - - - then yes, you are going to lose value as nobody wants to buy a car with problems - at least, not for the same price they could buy a trouble-free car.
Angel