OK thanks for the explanation, it is much clearer to me now.
Yes their are IR LEDs in many form factors so getting a direct replacement is not going to be hard.
However I do foresee some potential problems.
First off the amount of brightness you need in a IR emitter sending to a receiver compared with visible light that you look at is much greater. This might involve changing the current limiting resistor and you will also need to confirm that the LED's driver is up to supplying the extra current, as well as the impact on the battery life. As the forward voltage drop of an IR LED is lower than that of a visible LED you are going to get more current anyway.
The next problem is that of controlling the flashing rate, normally IR data is modulated at 38KH ( but can be between 32 to 42 KHz ), however on top of that you have the signal which consists of a number of pulses of this modulated signal. This is not the same as PWM and I don't think you can do it with PWM as that essentially is a free running autonomous system and you need to control every pulse of the LED precisely.
Hope that helps.