The length of time your light can run at a given brightness depends on the energy in the cell(s). If you have more than one cell, either in series or parallel, the total energy available is the sum of the energies that all the cells contain. Think of a battery as a tank of gas, which also contains a fixed amount of energy. Two tanks of the same size, twice the energy. Take it out fast or slow, you can in theory get the same amount of energy out of a given volume of gas.
The energy is the power times the time, which is the voltage times the current times the time. The current times the time is the "capacity", so for example the energy in a 3000mAh, 3.7 volt Li-ion cell is about 3.7 * 3000 = 11,100 mWh or 11.1 watt-hours. I say "about" because a number of factors modify this some -- the battery capacity is less when you consume the energy at a higher rate (discharge at a higher current), and the voltage isn't fixed at 3.7 or any other value but drops as the battery discharges. But it'll get you in the ballpark. So you can see that two non-rechargeable 1500mAh CR123A cells would have a bit less energy than a 3000mAh 18650 because the voltage of each of the CR123A cells is lower than the 18650 due to different chemistry. The practical effect of this depends on how efficiently the energy is extracted and converted to what the LED needs by the electronic circuitry in the flashlight. Decent flashlights usually have switching regulators which maintain about the same efficiency over a pretty wide range of voltages.
I've found that most of the flashlights I have that use either an 18650 or two CR123As have a buck type regulator. This requires the battery voltage to be a bit higher than the LED forward voltage of around 3-2-3.5 volts. A single 18650 reaches this level well before it's fully discharged, causing the regulator to quit working and the LED current to begin dropping. A few "high voltage" 18650 cells (ones that can be safely charged to 4.35 volts) stay above this level longer during the discharge period, but most will cause the light to begin dimming before all the the energy is extracted from the cell. This doesn't happen when two CR123A cells are used, because the series voltage never drops that low. That's the main possible down side to using a single 18650 cell, but it's not a problem if you can recharge the cell before it's more than partially discharged or if the dimming isn't a problem. It's often hard to detect even a 50% reduction in light level, and it's virtually unnoticeable if it happens slowly.
A very few lights seem to have a buck-boost regulator that can maintain the proper LED current as the battery voltage drops to, and below, the LED voltage. But these regulators are more complex and generally less efficient so they don't seem to be commonly used in flashlights.
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