Surprised no one pointed this out, but you can make flares any color you want to using some commands:
asw_flare_r #
asw_flare_g #
asw_flare_b #

replace # with any number 0-255. R is red, B is blue, G is green. Its client side, so only you will see the changes you make.

However, The color will reset everytime you start the game. If you want to make it stick around, open the folder where the game is installed and go here:
\reactivedrop\cfg

Inside this folder, find a config file called 'autoexec.cfg'
(if you can't find one, then make a new text file called 'autoexec.cfg'. Erase the .txt on the end, and you should be good to go.)

Open it with notepad. Any command you put in here will automatically run whenever you start the game- just put each command on a different row, and you're good to go.

Nice! Thank you for this guide and also for taking the time to help me out!

It's better to put the commands into newmapsettings.cfg instead of autoexec.cfg actually

Also, these are only clients cvars and can't be used server side. Server just doesn't recognise them.

nice