I would not create a lot of flight plans that use the same aircraft as you can not have the same aircraft in different places and with the number of flight plans you are creating the odds for duplicates increase drastically. Also the more AI traffic you have the slower your computer will run.
And I hope you are not using aircraft that are flyable in any of your flight plans as this will bring a system to a crawl.
I am pretty sure that somewhere in this forum you will find an example of what a flight plan should look like.
This is the most common error with flight plans. I usually download a few flight plans from world of AI and stick to airline flight plans as I know there will not be any duplicates. But every time you add a flight plan that is being used someplace else you have to make sure that the plane is not in flight at the time the other plan needs it. And do not forget time zones that is another common error people forget about. If I start a flight in a Eastern time zone say 10:00 and it is a four hour flight I can not start a flight in a Pacific time zone of 11:00 as the plane will still be in flight.
And like you said with the more plans you create the bigger the headache checking them all.
You will have less problems by limiting the number of AI flight plans you have running at any one time,