Appologies, I see what your saying now.
Mostly when I've seen people suggesting FIFO's they are talking purely first in is first out, so 3 objects would result in 3 items in the FIFO with the expectation that the first detection at the out position is the first item detected at the in position, this style of tracking is the problematic one that does not work.
Your suggesting filling the FIFO every pulse with default blank values and id's when an object is detected which is not what I thought you were saying.
One word of warning though, without knowing what is being tracked and over what distance and what type of conveyor.
A belt conveyor for example could have a different count of pulses over a distance, if the first object takes 100 pulses to get from one sensor to the next, the next object may take 103 pulses between the same sensors, the next 95, the next 101 and so on.
Depending on the size, gap and importance it may be needed to put in extra checking to ensure each detection is attributed to the correct object.