I wonder if I see an earlier version of this problem - I take the flight BA988 from London to Berlin a few times a year, and in some systems it will appear as BA0988 - possibly because some can handle 3 digit and some neee 4 digit flight numbers.
as you are a person who takes the same flight frequently , wont it be easier having the same flight number ? the flight companies should just make the flight numbers fixed for a fixed route, like local buses.
I'm a little confused by your comment - Airlines do re-use flight numbers - BA988 is always the BA flight from LHR to BER at around 19:30 (i.e. there will be a BA988 today, there was one yesterday, and there will be another tomorrow).
But to be honest, I'd also say it's not that useful for me personally. It's a lot easier to remember your destination and fight-time - (i.e. I'm on the 19:30 to Berlin) than a flight-number, and only once do I think there was ever the potential for confusion).
[You experience may vary, especially if you are are used to flying a busy flight corridor.]